Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy.

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV). Growth of the (101) face of TYMV crystals proceeded by two-dimensional nucleation. The molecular structure of the step edges and adsorption of individual virus particles and their aggregates on the crystalline surface were recorded. The surfaces of individual virions within crystals were visualized and seen to be quite distinctive with the hexameric and pentameric capsomers of the T = 3 capsids being clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions. In some cases areas of a single crystal surface were recorded in which were captured successive phases of the transition. We believe this provides the first visual record of a cooperative restructuring of the surface of a supramolecular crystal.     

Freezing of tissue-limits for the autoradiographic localization of diffusible substances

Frozen thin sections and sections from freeze-dried and embedded tissue are used for the autoradiographic localization of diffusible substances at the electron microscope level. The presence of ice crystals in such sections may limit the autoradiographic resolution. Ice crystals are formed during freezing and may grow during subsequent processing of tissue. The contribution of ice crystal growth to the final image was estimated by measuring the distribution of the ice crystal sizes in freeze-etch replicas and in sections from freeze-dried and embedded tissues. A surface layer (10-15 mu) without visible ice crystals was present in both preparations. Beneath this surface layer the diameter of ice crystals increased towards the interior with the same relationship between crystal size and distance from the surface in the freeze-etch preparation as in the freeze-dry preparation. Ice crystal growth occurring during a much longer time during freeze-drying compared to freeze-etching does not significantly contribute to the final image in the electron microscope. The formation of ice crystals during freezing determines to a large extent the image (and therefore the autoradiographic resolution) of freeze-dry preparations and this probably holds also for thin cryosections of which examples are given.     

Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation

The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores as well as the spatial distribution of Y-junctions across entire retinae. We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals. In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery. In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion. Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries. In contrast to paradigmatic models of fate specification in mostly motionless cell packings, this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.     

Prediction of the conformation of ice-nucleation protein by conformational energy calculation

The active conformation of an ice-nucleation protein, whose major portion consists of a long polypeptide segment of nearly repetitive octapeptides, is predicted by the analyses of conformational energy and the mechanism of crystal growth. The protein ideally has an exact octapeptide repetition and is assumed to have a helical conformation. The present study searched for low-energy helical conformations and each of the obtained low-energy conformations examined as to whether it has a surface structure that can promote crystal formation. Two conformations obtained were good candidates for an ice nucleus. Both were found to have on their surfaces an arrangement of hydrogen-bonding sites, which fits well with those of hydrogen bonds in hexagonal ice crystal. Further, one of the two conformations had a hexagonal conformational symmetry consistent with the hexagonal ice crystal structure. The other conformation had a pentagonal conformational symmetry that could enable the growth of an ice crystal--dendritic polycrystalline snow crystal--which grows on metastable cubic ice.     

In situ observation of elementary growth processes of protein crystals by advanced optical microscopy

To start systematically investigating the quality improvement of protein crystals, the elementary growth processes of protein crystals must be first clarified comprehensively. Atomic force microscopy (AFM) has made a tremendous contribution toward elucidating the elementary growth processes of protein crystals and has confirmed that protein crystals grow layer by layer utilizing kinks on steps, as in the case of inorganic and low-molecular-weight compound crystals. However, the scanning of the AFM cantilever greatly disturbs the concentration distribution and solution flow in the vicinity of growing protein crystals. AFM also cannot visualize the dynamic behavior of mobile solute and impurity molecules on protein crystal surfaces. To compensate for these disadvantages of AFM, in situ observation by two types of advanced optical microscopy has been recently performed. To observe the elementary steps of protein crystals noninvasively, laser confocal microscopy combined with differential interference contrast microscopy (LCM-DIM) was developed. To visualize individual mobile protein molecules, total internal reflection fluorescent (TIRF) microscopy, which is widely used in the field of biological physics, was applied to the visualization of protein crystal surfaces. In this review, recent progress in the noninvasive in situ observation of elementary steps and individual mobile protein molecules on protein crystal surfaces is outlined.     

Heat denaturation of crystalline and dissolved leghemoglobin

Heat transitions in crystals of leghemoglobin (LH) are studied by means of scanning microcalorimetry and microscopy. It has been found that LH crystals do not melt and their loss of crystal lattice is due to the denaturation of protein globules inside the crystal. Peculiarities of the crystal state (as compared to the solution) are shown in an increase in the cooperative character of heat transition and relaxation time of the system. Subsequent consideration of different variants of correlation of two stages of heat absorption by LH crystals made it possible to determine the type of physical process proceeding in the object by the shape of calorimetric curve. Both observed peaks of heat absorption were grouped with intramolecular processes of different thermodynamic properties. The first peak of heat absorption is a manifestation of intramolecular mobility, both of individual protein segments in relation to each other and of individual segments of alpha-helical regions. Thus microcalorimetry allows a study of peculiar intramolecular dynamics of globular proteins precisely in the crystal state, because the crystal as if synchronizes the movement of individual molecules at the expense of the unification of their kinetic energy, surroundings and mutual orientation.     

The Role of Grain Boundaries on Ionic Defect Migration in Metal Halide Perovskites

Halide perovskites are emerging as revolutionary materials for optoelectronics. Their ionic nature and the presence of mobile ionic defects within the crystal structure have a dramatic influence on the operation of thin‐film devices such as solar cells, light‐emitting diodes, and transistors. Thin films are often polycrystalline and it is still under debate how grain boundaries affect the migration of ions and corresponding ionic defects. Laser excitation during photoluminescence (PL) microscopy experiments leads to formation and subsequent migration of ionic defects, which affects the dynamics of charge carrier recombination. From the microscopic observation of lateral PL distribution, the change in the distribution of ionic defects over time can be inferred. Resolving the PL dynamics in time and space of single crystals and thin films with different grain sizes thus, provides crucial information about the influence of grain boundaries on the ionic defect movement. In conjunction with experimental observations, atomistic simulations show that defects are trapped at the grain boundaries, thus inhibiting their diffusion. Hence, with this study, a comprehensive picture highlighting a fundamental property of the material is provided while also setting a theoretical framework in which the interaction between grain boundaries and ionic defect migration can be understood.     

Analysis of edge birefringence.

We present an experimental and theoretical study of the phenomenon of edge birefringence that appears near boundaries of transparent objects which are observed with high extinction and high resolution polarized light microscopy. As test objects, thin flakes of isotropic KCl crystals were immersed in media of various refractive indices. The measured retardation near crystal edges increased linearly with both the crystal thickness (tested between 0.3 and 1 micron), and the difference in refractive indices n between crystal (n = 1.49) and immersion liquids (n between 1.36 and 1.62). The specific edge birefringence, i.e., the retardation per thickness and per refractive index difference, is 0.029 on the high refractive index side of the boundary and -0.015 on the low refractive index side. The transition through zero birefringence specifies the position of a boundary at a much higher precision than predicted by the diffraction limit of the optical setup. The theoretical study employs a ray tracing procedure modeling the change in phase and polarization of rays passing through the specimen. We find good agreement between the model calculations and the experimental results indicating that edge birefringence can be attributed to the change in polarization of light that is refracted and reflected by dielectric interfaces.     

A high-resolution electron microscope study of synthetic and biological carbonated apatites

A series of synthetic carbonated apatites and human dental enamels characterized by chemical analysis, infrared spectroscopy, and X-ray diffraction was studied using high-resolution transmission electron microscopy. Steps on the surfaces of apatite crystals, often only a few unit cells high and occasionally one unit cell high, were observed by their Fresnel diffraction contrast. Highly substituted synthetic carbonated apatites appeared to have more irregular and finer-textured surface features than materials with less carbonate substitution. The surface features of enamel apatite crystal were also irregular, but surface steps were less frequently aligned in crystallographic directions. Complex strain fields due to radiation damage centers were observed in some crystals and the fine structure of dislocations and grain boundaries in synthetic apatites was resolved at high magnification. Experimental lattice-image contrasts, in favorable circumstances, could be matched to computer-simulated images and were found to contain detail at near atomic resolution, around 2.0-2.5 A.     

抗冻糖蛋白溶液中冰晶生长速率的研究

在分析了溶液中抗冻糖蛋白与冰晶表面的相互作用的基础上,提出了在抗冻糖蛋白溶液中冰晶沿c轴方向生长的理论。给出了冰晶在抗冻糖蛋白溶液中生长速率的定量计算,而且理论值与实验结果有较好的符合,解释了冰晶在抗冻糖蛋白溶液中生长速度和生长习性的各向异性。     

Real-time evaluation of macromolecular surface modified quartz crystal resonant sensors under cryogenic stress for biological applications

This study presents a novel auto-gain-control based quartz acoustic sensor technology capable of constant quartz crystal operation when cycled between ambient (22 degrees C) and cryogenic temperatures (-196 degrees C), afforded by direct exposure of crystals to bulk liquid nitrogen. The real-time frequency response profiles due to freeze-thaw cycling on crystals of differing surface finish and two model macromolecular surface coatings were studied in order to determine surface events such as water uptake. The quartz crystal surface finishes used were optically polished or lapped to one of two surface finishes. These were used as control native gold electrodes, and these surfaces were further coated with bovine serum albumin or the tri-block copolymer, poloxamer-188 as model macromolecular surface architectures. Crystals were snap frozen in liquid nitrogen and allowed to return to ambient temperature under controlled conditions. The processes of ice formation, thawing and evaporation were followed in real-time and comparisons were made between the test samples in order to assess the capability of this technique for sensing changes in surface characteristics such as the entrapment of water.     

Mechanism of Ice Growth in a Batch Crystallizer with an External Cooler for Freeze Concentration

Two mechanisms of ice crystal growth were found in a batch crystallizer with an external cooler, that contained a large amount of ice crystals. With the first mechanism, the ice crystals grew larger by the usual kind of growth, governed by heat or mass transfer resistance, and with the second, the ice crystals agglomerated and the agglomerate fused into a very large ice crystal (1 ~3mm in diameter). The conditions in which the second mechanism prevails were investigated extensively. The second mechanism occurred not because of the high concentration of ice crystals in the crystallizer but because of long residence time. Large ice crystal agglomerates were not produced when extremely small ice crystals were formed in the crystallizer at the start of the experiment.     

Relationships between ice crystal size, water content and proton NMR relaxation times in cells

Biological specimens were frozen under controlled conditions. We questioned how the size of ice crystals, as measured in cryosectioned and cryoadsorbed sections of these biological specimens, relates to the water content and to the proton NMR relaxation times (T1 and T2) of the unfrozen specimens. The results permit the following conclusions: After rapid freezing in liquid propane cooled in a liquid nitrogen bath, the average size of ice crystals at distances of 150 microns or more from the surface of a particular tissue was always the same. Thus, the average size of the ice crystals was found to be characteristic of the type of biological tissue studied. Linear regression analysis showed average ice crystal size to have a significant correlation coefficient to T1 relaxation time and to water content. Specifically ice crystal size increased with T1 relaxation time and with water content. Multiple regression and path analysis demonstrated a positive correlation between the T1 relaxation time and the ice crystal size variation. Path analysis showed that both water content and T2 relaxation time were less directly correlated with ice crystal size. The findings from the path analysis and other observations show that the average size of ice crystals in subcellular compartments is best predicted by the proton T1 relaxation time. A working model is put forth to explain differences in ice crystal size observed between specimens enriched in globular or in parallel filamentous proteins.     

A model for binding of an antifreeze polypeptide to ice.

A model is proposed, based on recent peptide analog and ice crystal etching studies, whereby an alanine-rich, alpha-helical antifreeze polypeptide (AFP) from the winter flounder inhibits the growth of ice crystals by hydrogen bonding of Thr, Asn, and Asp side chains in a specific pattern to the [2021] hexagonal bipyramidal planes of ice. It is further suggested that this mode of binding is unidirectional, maximizing opportunities for packing of AFPs on the ice surface, and that ice crystal growth inhibition occurs by a two-step mechanism involving hydrogen bonding and hydrophobic interpeptide interactions.     

Conjugation of type I antifreeze protein to polyallylamine increases thermal hysteresis activity

Antifreeze proteins (AFPs) are ice binding proteins found in some plants, insects, and Antarctic fish allowing them to survive at subzero temperatures by inhibiting ice crystal growth. The interaction of AFPs with ice crystals results in a difference between the freezing and melting temperatures, termed thermal hysteresis, which is the most common measure of AFP activity. Creating antifreeze protein constructs that reduce the concentration of protein needed to observe thermal hysteresis activities would be beneficial for diverse applications including cold storage of cells or tissues, ice slurries used in refrigeration systems, and food storage. We demonstrate that conjugating multiple type I AFPs to a polyallylamine chain increases thermal hysteresis activity compared to the original protein. The reaction product is approximately twice as active when compared to the same concentration of free proteins, yielding 0.5 °C thermal hysteresis activity at 0.3 mM protein concentration. More impressively, the amount of protein required to achieve a thermal hysteresis of 0.3 °C is about 100 times lower when conjugated to the polymer (3 μM) compared to free protein (300 μM). Ice crystal morphologies observed in the presence of the reaction product are comparable to those of the protein used in the conjugation reaction.     

Direct evidence for antifreeze glycoprotein adsorption onto an ice surface

Aqueous solutions of antifreeze glycoproteins (AFGP) exhibit hysteresis between the freezing and melting temperatures. Several recent studies on the mechanism of function of this protein system suggest that a likely model is for the antifreeze molecules to be adsorbed onto the surface of the crystals. However, direct proof of the presence of adsorbed AFGP has eluded previous researchers. In the present study, enhanced surface second-harmonic generation (SSHG) was observed in the presence of an active AFGP solution in contact with a pure single crystal of ice. The enhancement of SSHG is a positive indication that active AFGP molecules adsorb to the surface of ice crystals.     

Ice Morphology: Fundamentals and Technological Applications in Foods

Freezing is the process of ice crystallization from supercooled water. Ice crystal morphology plays an important role in the textural and physical properties of frozen and frozen-thawed foods and in processes such as freeze drying, freeze concentration, and freeze texturization. Size and location of ice crystals are key in the quality of thawed tissue products. In ice cream, smaller ice crystals are preferred because large crystals results in an icy texture. In freeze drying, ice morphology influences the rate of sublimation and several morphological characteristics of the freeze-dried matrix as well as the biological activity of components (e.g., in pharmaceuticals). In freeze concentration, ice morphology influences the efficiency of separation of ice crystals from the concentrated solution. The cooling rate has been the most common variable controlling ice morphology in frozen and partly frozen systems. However, several new approaches show promise in controlling nucleation (consequently, ice morphology), among them are the use of ice nucleation agents, antifreeze proteins, ultrasound, and high pressure. This paper summarizes the fundamentals of freezing, methods of observation and measurement of ice morphology, and the role of ice morphology in technological applications.     

Understanding the mechanism of ice binding by type III antifreeze proteins

Type III antifreeze proteins (AFPs) are present in the body fluids of some polar fishes where they inhibit ice growth at subzero temperatures. Previous studies of the structure of type III AFP by NMR and X-ray identified a remarkably flat surface on the protein containing amino acids that were demonstrated to be important for interaction with ice by mutational studies. It was proposed that this protein surface binds onto the (1 0 [\bar 1] 0) plane of ice with the key amino acids interacting directly with the water molecules in the ice crystal. Here, we show that the mechanism of type III AFP interaction with ice crystals is more complex than that proposed previously. We report a high-resolution X-ray structure of type III AFP refined at 1.15 A resolution with individual anisotropic temperature factors. We report the results of ice-etching experiments that show a broad surface coverage, suggesting that type III AFP binds to a set of planes that are parallel with or inclined at a small angle to the crystallographic c-axis of the ice crystal. Our modelling studies, performed with the refined structure, confirm that type III AFP can make energetically favourable interactions with several ice surfaces.     

Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice

Glaciers accumulate airborne microorganisms year by year and thus are good archives of microbial communities and their relationship to climatic and environmental changes. Hypotheses have focused on two possible drivers of microbial community composition in glacier systems. One is aeolian deposition, in which the microbial load by aerosol, dust, and precipitation events directly determines the amount and composition of microbial species in glacier ice. The other is postdepositional selection, in which the metabolic activity in surface snow causes microbial community shifts in glacier ice. An additional possibility is that both processes occur simultaneously. Aeolian deposition initially establishes a microbial community in the ice, whereas postdeposition selection strengthens the deposition patterns of microorganisms with the development of tolerant species in surface snow, resulting in varying structures of microbial communities with depth. In this minireview, we examine these postulations through an analysis of physical–chemical and biological parameters from the Malan and Vostok ice cores, and the Kuytun 51 Glacial surface and deep snow. We discuss these and other recent results in the context of the hypothesized mechanisms driving microbial community succession in glaciers. We explore our current gaps in knowledge and point out future directions for research on microorganisms in glacial ecosystems.     

Visualization of intracellular ice crystals formed in very rapidly frozen cells at −27 °C

Tumor cells of an ascites sarcoma of rat were primarily frozen very rapidly with the original host ascitic fluid at ?27 °C by the spraying method. Frozen specimens were fractured and replicated at about ?100 °C under vacuum by a special spray-sandwich method for freeze-etching, and the morphological appearance of ice crystals formed in and around the frozen cells were observed by electron microscopy.The cells cooled very rapidly at ?27 °C actually froze intracellularly, and intracellular ice crystals ranged from 0.03 to 0.5 μm in grain size due to the initial freezing rate of the specimens. In the cells having granulous intracellular ice crystals less than 0.05 μm in grain size, cytoplasmic organelles seemed to maintain their original structures.We suggested in our previous report that these tumor cells, frozen very rapidly at temperatures above ?30 °C, survived intracellular freezing as long as they remained translucent, and optically no ice crystals appeared within them, as seen in intact unfrozen cells. It may therefore be concluded that the tumor cells frozen very rapidly at temperatures near ?30 °C actually freeze intracellularly and probably maintain their viability as long as the size of individual intracellular ice-crystals is kept smaller than 0.05 μm, although the exact critical size of innocuous intracellular ice crystals is uncertain.