Simulation-based optimisation of thermodynamic conditions in the ESEM for dynamical in-situ study of spherical polyelectrolyte complex particles in their native state

Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state

The challenge of in-situ handling and high-resolution low-dose imaging of intact, sensitive and wet samples in their native state at nanometer scale, including live samples is met by Advanced Environmental Scanning Electron Microscopy (A-ESEM). This new generation of ESEM utilises machine learning-based optimization of thermodynamic conditions with respect to sample specifics to employ a low temperature method and an ionization secondary electron detector with an electrostatic separator. A modified electron microscope was used, equipped with temperature, humidity and gas pressure sensors for in-situ and real-time monitoring of the sample. A transparent ultra-thin film of ionic liquid is used to increase thermal and electrical conductivity of the samples and to minimize sample damage by free radicals. To validate the power of the new method, we analyze condensed mitotic metaphase chromosomes to reveal new structural features of their perichromosomal layer, and the organization of chromatin fibers, not observed before by any microscopic technique. The ability to resolve nano-structural details of chromosomes using A-ESEM is validated by measuring gold nanoparticles with achievable resolution in the lower nanometre units.

Mathematical-Physics Analyses of the Nozzle Shaping at the Aperture Gas Outlet into Free Space under ESEM Pressure Conditions

The paper presents a methodology that combines experimental measurements and mathematical-physics analyses to investigate the flow behavior in a nozzle-equipped aperture associated with the solution of its impact on electron beam dispersion in an environmental scanning electron microscope (ESEM). The shape of the nozzle significantly influences the character of the supersonic flow beyond the aperture, especially the shape and type of shock waves, which are highly dense compared to the surrounding gas. These significantly affect the electron scattering, which influences the resulting image. This paper analyzes the effect of aperture and nozzle shaping under specific low-pressure conditions and its impact on the electron dispersion of the primary electron beam.

Mathematical Physics Analysis of Nozzle Shaping at the Gas Outlet from the Aperture to the Differentially Pumped Chamber in Environmental Scanning Electron Microscopy (ESEM)

A combination of experimental measurement preparations using pressure and temperature sensors in conjunction with the theory of one-dimensional isentropic flow and mathematical physics analyses is presented as a tool for analysis in this paper. Furthermore, the subsequent development of a nozzle for use in environmental electron microscopy between the specimen chamber and the differentially pumped chamber is described. Based on experimental measurements, an analysis of the impact of the nozzle shaping located behind the aperture on the character of the supersonic flow and the resulting dispersion of the electron beam passing through the differential pumped chamber is carried out on the determined pressure ratio using a combination of theory and mathematical physics analyses. The results show that nozzle shapes causing under-expanded gas outflow from the aperture to the nozzle have a worse impact on the dispersion of the primary electron beam. This is due to the flow velocity control. The controlled reduction in the static pressure curve on the primary electron beam path thus causes a significantly higher course of electron dispersion values than variants with shapes causing over-expanded gas outflow.

The Impact of Nozzle Opening Thickness on Flow Characteristics and Primary Electron Beam Scattering in an Environmental Scanning Electron Microscope

This paper describes the methodology of combining experimental measurements with mathematical-physics analyses in the investigation of flow in the aperture and nozzle. The aperture and nozzle separate the differentially pumped chamber from the specimen chamber in an environmental scanning electron microscope (ESEM). Experimental measurements are provided by temperature and pressure sensors that meet the demanding conditions of cryogenic temperature zones and low pressures. This aperture maintains the required pressure difference between the chambers. Since it separates the large pressure gradient, critical flow occurs on it and supersonic gas flow with the characteristic properties of critical flow in the state variables occurs behind it. As a primary electron beam passes through the differential pumped chamber and the given aperture, the aperture is equipped with a nozzle. The shape of the nozzle strongly influences the character of the supersonic flow. The course of state variables is also strongly influenced by this shape; thus, it affects the number of collisions the primary beam's electrons have with gas molecules, and so the resulting image. This paper describes experimental measurements made using sensors under laboratory conditions in a specially created experimental chamber. Then, validation using mathematical-physical analysis in the Ansys Fluent system is described.

Impact of Supersonic Flow in Scintillator Detector Apertures on the Resulting Pumping Effect of the Vacuum Chambers

The article describes the combination of experimental measurements with mathematical-physics analyses in flow investigation in the chambers of the scintillator detector, which is a part of the environmental scanning electron microscope. The chambers are divided with apertures by small openings that keep the desirable pressure differences between three chambers: The specimen chamber, the differentially pumped intermediate chamber, and the scintillator chamber. There are conflicting demands on these apertures. On the one hand, the diameter of the apertures must be as big as possible so that they incur minimal losses of the passing secondary electrons. On the other hand, it is possible to magnify the apertures only to a certain extent so the rotary and turbomolecular vacuum pump can maintain the required operating pressures in separate chambers. The article describes the combination of experimental measurement using an absolute pressure sensor and mathematical physics analysis to map all the specifics of the emerging critical supersonic flow in apertures between the chambers. Based on the experiments and their tuned analyses, the most effective variant of combining the sizes of each aperture concerning different operating pressures in the detector is determined. The situation is made more difficult by the described fact that each aperture separates a different pressure gradient, so the gas flow through each aperture has its own characteristics with a different type of critical flow, and they influence each other, thereby influencing the final passage of secondary electrons detected by the scintillator and thus affecting the resulting displayed image.

Slip Flow Analysis in an Experimental Chamber Simulating Differential Pumping in an Environmental Scanning Electron Microscope

This paper describes the combination of experimental measurements with mathematical-physical analysis during the investigation of flow in an aperture at low pressures in a prepared experimental chamber. In the first step, experimental measurements of the pressure in the specimen chamber and at its outlet were taken during the pumping of the chamber. This process converted the atmospheric pressure into the operating pressure typical for the current AQUASEM II environmental electron microscope at the ISI of the CAS in Brno. Based on these results, a mathematical-physical model was tuned in the Ansys Fluent system and subsequently used for mathematical-physical analysis in a slip flow regime on a nozzle wall at low pressure. These analyses will be used to fine-tune the experimental chamber. Once the chamber is operational, it will be possible to compare the results obtained from the experimental measurements of the nozzle wall pressure, static pressure, total pressure and temperature from the nozzle axis region in supersonic flow with the results obtained from the mathematical-physical analyses. Based on the above comparative analyses, we will be able to determine the realistic slip flow at the nozzle wall under different conditions at the continuum mechanics boundary.

Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development

Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).

ESEM Methodology for the Study of Ice Samples at Environmentally Relevant Subzero Temperatures: "Subzero ESEM"

Frozen aqueous solutions are an important subject of study in numerous scientific branches including the pharmaceutical and food industry, atmospheric chemistry, biology, and medicine. Here, we present an advanced environmental scanning electron microscope methodology for research of ice samples at environmentally relevant subzero temperatures, thus under conditions in which it is extremely challenging to maintain the thermodynamic equilibrium of the specimen. The methodology opens possibilities to observe intact ice samples at close to natural conditions. Based on the results of ANSYS software simulations of the surface temperature of a frozen sample, and knowledge of the partial pressure of water vapor in the gas mixture near the sample, we monitored static ice samples over several minutes. We also discuss possible artifacts that can arise from unwanted surface ice formation on, or ice sublimation from, the sample, as a consequence of shifting conditions away from thermodynamic equilibrium in the specimen chamber. To demonstrate the applicability of the methodology, we characterized how the true morphology of ice spheres containing salt changed upon aging and the morphology of ice spheres containing bovine serum albumin. After combining static observations with the dynamic process of ice sublimation from the sample, we can attain images with nanometer resolution.

Application of Prandtl's Theory in the Design of an Experimental Chamber for Static Pressure Measurements

Pumping in vacuum chambers is part of the field of environmental electron microscopy. These chambers are separated from each other by a small-diameter aperture that creates a critical flow in the supersonic flow regime. The distribution of pressure and shock waves in the path of the primary electron beam passing through the differentially pumped chamber has a large influence on the quality of the resulting microscope image. As part of this research, an experimental chamber was constructed to map supersonic flow at low pressures. The shape of this chamber was designed using mathematical–physical analyses, which served not only as a basis for the design of its geometry, but especially for the correct choice of absolute and differential pressure sensors with respect to the cryogenic temperature generated in the supersonic flow. The mathematical and physical analyses presented here map the nature of the supersonic flow with large gradients of state variables at low pressures at the continuum mechanics boundary near the region of free molecule motion in which the Environmental Electron Microscope and its differentially pumped chamber operate, which has a significant impact on the resulting sharpness of the final image obtained by the microscope. The results of this work map the flow in and behind the Laval nozzle in the experimental chamber and are the initial basis that enabled the optimization of the design of the chamber based on Prandtl’s theory for the possibility of fitting it with pressure probes in such a way that they can map the flow in and behind the Laval nozzle.

Correlative Light-Environmental Scanning Electron Microscopy of Plasma Membrane Efflux Carriers of Plant Hormone Auxin

Fluorescence light microscopy provided convincing evidence for the domain organization of plant plasma membrane (PM) proteins. Both peripheral and integral PM proteins show an inhomogeneous distribution within the PM. However, the size of PM nanodomains and protein clusters is too small to accurately determine their dimensions and nano-organization using routine confocal fluorescence microscopy and super-resolution methods. To overcome this limitation, we have developed a novel correlative light electron microscopy method (CLEM) using total internal reflection fluorescence microscopy (TIRFM) and advanced environmental scanning electron microscopy (A-ESEM). Using this technique, we determined the number of auxin efflux carriers from the PINFORMED (PIN) family (NtPIN3b-GFP) within PM nanodomains of tobacco cell PM ghosts. Protoplasts were attached to coverslips and immunostained with anti-GFP primary antibody and secondary antibody conjugated to fluorochrome and gold nanoparticles. After imaging the nanodomains within the PM with TIRFM, the samples were imaged with A-ESEM without further processing, and quantification of the average number of molecules within the nanodomain was performed. Without requiring any post-fixation and coating procedures, this method allows to study details of the organization of auxin carriers and other plant PM proteins.

Immobilized Cell Physiology Imaging and Stabilization of Enzyme Cascade Reaction Using Recombinant Cells Escherichia coli Entrapped in Polyelectrolyte Complex Beads by Jet Break-Up Encapsulator

A novel, high performance, and scalable immobilization protocol using a laminar jet break-up technique was developed for the production of polyelectrolyte complex beads with entrapped viable Escherichia coli cells expressing an enzyme cascade of alcohol dehydrogenase, enoate reductase, and cyclohexanone monooxygenase. A significant improvement of operational stability was achieved by cell immobilization, which was manifested as an almost two-fold higher summative product yield of 63% after five cascade reaction cycles as compared to the yield using free cells of 36% after the maximum achievable number of three cycles. Correspondingly, increased metabolic activity was observed by multimodal optical imaging in entrapped cells, which was in contrast to a complete suppression of cell metabolism in free cells after five reaction cycles. Additionally, a high density of cells entrapped in beads had a negligible effect on bead permeability for low molecular weight substrates and products of cascade reaction.

Dynamical in-situ observation of the lyophilization and vacuum-drying processes of a model biopharmaceutical system by an environmental scanning electron microscope

The paper discusses the real-time monitoring of the changing sample morphology during the entire lyophilization (freeze-drying) and vacuum-drying processes of model biopharmaceutical solutions by using an environmental scanning electron microscope (ESEM); the device's micromanipulators were used to study the interior of the samples in-situ without exposing the samples to atmospheric water vapor. The individual collapse temperatures (T_c) of the formulations, pure bovine serum albumin (BSA) and BSA/sucrose mixtures, ranged from -5 to -29 °C. We evaluated the impact of the freezing method (spontaneous freezing, controlled ice nucleation, and spray freezing) on the morphologies of the lyophiles at the constant drying temperature of -20 °C. The formulations with T_c above -20 °C resulted in the lyophiles' morphologies significantly dependent on the freezing method. We interpret the observations as an interplay of the freezing rates and directionalities, both of which markedly influence the morphologies of the frozen formulations, and, subsequently, the drying process and the mechanical stability of the freeze-dried cake. The formulation with T_c below -20 °C yielded a collapsed cake with features independent of the freezing method. The vacuum-drying produced a material with a smooth and pore-free surface, where deep cracks developed at the end of the process.