Editors' Roundup: June 2022.

This Commentary describes the June 2022 installment of the "Editors' Roundup" feature. The Editors' Roundup is a multi-author collective description of recently published biophysical research contributed by editorial board members of different journals with a bonafide interest in publishing biophysical content. This Commentary contains a series of personal recommendations for articles appearing in the following journals, Biophysics and Physicobiology, European Biophysics Journal, Cell Biochemistry and Biophysics, and Biophysical Reviews.

Smartphone-Based Portable Bioluminescence Imaging System Enabling Observation at Various Scales from Whole Mouse Body to Organelle.

Current smartphones equipped with high-sensitivity and high-resolution sensors in the camera can respond to the needs of low-light imaging, streaming acquisition, targets of various scales, etc. Therefore, a smartphone has great potential as an imaging device even in the scientific field and has already been introduced into biomolecular imaging using fluorescence tags. However, owing to the necessity of an excitation light source, fluorescence methods impair its mobility. Bioluminescence does not require illumination; therefore, imaging with a smartphone camera is compact and requires minimal devices, thus making it suitable for personal and portable imaging devices. Here, we report smartphone-based methods to observe biological targets in various scales using bioluminescence. In particular, we demonstrate, for the first time, that bioluminescence can be observed in an organelle in a single living cell using a smartphone camera by attaching a detachable objective lens. Through capturing color changes with the camera, changes in the amount of target molecules was detected using bioluminescent indicators. The combination of bioluminescence and a mobile phone makes possible a compact imaging system without an external light source and expands the potential of portable devices.

Biophysical Reviews' "Meet the Editors Series"-a profile of Kuniaki Nagayama: encounters and leaps in a transborder journey through biophysics.

In this second instalment of the Biophysical Reviews' Meet the Editors Series we hear the story of Prof. Kuniaki Nagayama, one of the five Executive Editors of Biophysical Reviews.

Transmission Electron Microscope Using a Linear Accelerator.

High-voltage transmission electron microscopes (HVTEMs), which can visualize internal structures of micron thick samples, intrinsically have large instrument sizes because of the static voltage isolation. In this Letter, we develop a compact HVTEM, employing a linear accelerator, a subpicosecond beam chopper, and a linear decelerator. 100 kV electrons initially accelerated by a static field are accelerated at radio frequency (rf) up to 500 kV, transmitting through the sample and finally rf decelerated down to 200 kV to be imaged through a 200 kV energy filter. 500 kV imaging, as well as subnanometer resolution at 200 kV, have been demonstrated.

Cathodoluminescence and Electron-Induced Fluorescence Enhancement of Enhanced Green Fluorescent Protein.

Becaues the spatial resolution of fluorescence microscopy is not high enough to study the molecular level of relationship between the structure and function of biological specimens, correlative light and electron microscopy has been used for this purpose. Another possibility for a high-resolution light microscopy is cathodoluminescence microscopy. Here, we report a new phenomenon, the electron-induced activation of luminescence (cathodoluminescence) and electron-enhanced fluorescence for the enhanced green fluorescent protein (EGFP). This was found using our recently developed hybrid fluorescence and electron microscopy. Contrary to the past reports, which showed a degradation of organic compounds by electron irradiation, stable cathodoluminescence emitted from an organic molecule, EGFP, has been observed using the hybrid microscopy. Addition of the glycerol promoted the fluorescence enhancement of EGFP probably due to the change in the electronic state density of excitation channels from the ground to the excited state or of relaxation channels from the excited to the emission state. Stable cathodoluminescence and enhanced fluorescence of the EGFP may introduce a cathodoluminescence microscopy, which will increase the variety of the imaging to investigate the biological compounds.

Multi-pore carbon phase plate for phase-contrast transmission electron microscopy.

A new fabrication method of carbon based phase plates for phase-contrast transmission electron microscopy is presented. This method utilizes colloidal masks to produce pores as well as disks on thin carbon membranes for phase modulation. Since no serial process is involved, carbon phase plate membranes containing hundreds of pores can be mass-produced on a large scale, which allows "disposal" of contaminated or degraded phase modulating objects after use. Due to the spherical shape of the mask colloid particles, the produced pores are perfectly circular. The pore size and distribution can be easily tuned by the mask colloid size and deposition condition. By using the stencil method, disk type phase plates can also be fabricated on a pore type phase plate. Both pore and disk type phase plates were tested by measuring amorphous samples and confirmed to convert the sinus phase contrast transfer function to the cosine shape.

Structural characterization of the mechanosensitive channel candidate MCA2 from Arabidopsis thaliana.

Mechanosensing in plants is thought to be governed by sensory complexes containing a Ca²âº-permeable, mechanosensitive channel. The plasma membrane protein MCA1 and its paralog MCA2 from Arabidopsis thaliana are involved in mechanical stress-induced Ca²âº influx and are thus considered as candidates for such channels or their regulators. Both MCA1 and MCA2 were functionally expressed in Sf9 cells using a baculovirus system in order to elucidate their molecular natures. Because of the abundance of protein in these cells, MCA2 was chosen for purification. Purified MCA2 in a detergent-solubilized state formed a tetramer, which was confirmed by chemical cross-linking. Single-particle analysis of cryo-electron microscope images was performed to depict the overall shape of the purified protein. The three-dimensional structure of MCA2 was reconstructed at a resolution of 26 Å from 5,500 particles and appears to comprise a small transmembrane region and large cytoplasmic region.

Hybrid fluorescence and electron cryo-microscopy for simultaneous electron and photon imaging.

Integration of fluorescence light and transmission electron microscopy into the same device would represent an important advance in correlative microscopy, which traditionally involves two separate microscopes for imaging. To achieve such integration, the primary technical challenge that must be solved regards how to arrange two objective lenses used for light and electron microscopy in such a manner that they can properly focus on a single specimen. To address this issue, both lateral displacement of the specimen between two lenses and specimen rotation have been proposed. Such movement of the specimen allows sequential collection of two kinds of microscopic images of a single target, but prevents simultaneous imaging. This shortcoming has been made up by using a simple optical device, a reflection mirror. Here, we present an approach toward the versatile integration of fluorescence and electron microscopy for simultaneous imaging. The potential of simultaneous hybrid microscopy was demonstrated by fluorescence and electron sequential imaging of a fluorescent protein expressed in cells and cathodoluminescence imaging of fluorescent beads.

Biological applications of phase-contrast electron microscopy.

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

Visualizing virus assembly intermediates inside marine cyanobacteria.

Cyanobacteria are photosynthetic organisms responsible for ∼25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms.

Substrate-specific structural rearrangements of human Dicer.

Dicer has a central role in RNA-interference pathways by cleaving double-stranded RNAs (dsRNAs) to produce small regulatory RNAs. Human Dicer can process long double-stranded and hairpin precursor RNAs to yield short interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. Previous studies have shown that pre-miRNAs are cleaved more rapidly than pre-siRNAs in vitro and are the predominant natural Dicer substrates. We have used EM and single-particle analysis of Dicer-RNA complexes to gain insight into the structural basis for human Dicer's substrate preference. Our studies show that Dicer traps pre-siRNAs in a nonproductive conformation, whereas interactions of Dicer with pre-miRNAs and dsRNA-binding proteins induce structural changes in the enzyme that enable productive substrate recognition in the central catalytic channel. These findings implicate RNA structure and cofactors in determining substrate recognition and processing efficiency by human Dicer.

Non-acid-fastness in Mycobacterium tuberculosis ΔkasB mutant correlates with the cell envelope electron density.

The acid-fastness is the most important and the most specific characteristics in mycobacteria, the mechanism of which is not clear but may be attributed to the lipid rich cell wall of this bacterium. While the exact component(s) responsible for this staining method remained unidentified, a Mycobacterium tuberculosis mutant, attenuated strain that produced shorter mycolic acids with defects in trans-cyclopropanation was shown to be acid fast negative. In this study, we examined the ultrastructure of the cell envelope (CE) of the mutant strain ΔkasB (missing a beta-ketoacyl-ACP synthase involved in mycolic acid biosynthesis), the parental CDC1551 (wild type strain) and kasB complemented strain, and compared ultrastructural differences among them with conventional transmission electron microscopy (TEM) and cryo-transmission electron microscopy (CEM). Conventional TEM revealed that there were no detectable differences in the thickness of the cell envelope among three strains (wild-type: 43.35 ± 6.13 nm; ΔkasB: 45.98 ± 11.32 nm; complement: 40.71 ± 6.3 nm). However, CEM data demonstrated that the region between the inner and outer membranes of the mutant strain, which is composed mainly of cell wall anchored mycolic acids (MA), showed a significant decrease in electron density as compared to the wild type and kasB complement strain (567.1 ± 372.7 vs. 301.4 ± 262.1, or vs. 235.2 ± 174.9, p < 0.02 or p < 0.001, respectively). These results suggested that altered MA patterns in the kasB mutant may have affected the packing of the lipid rich layer of the M. tuberculosis cell envelope, resulting in a reduced electron density of this layer as seen by CEM and loss of acid-fastness in light microscopical observation, and we propose a novel model of the cell envelope structure in tubercle bacilli.

Direct observation of biological molecules in liquid by environmental phase-plate transmission electron microscopy.

We have been developing a combination method for environmental TEM (E-TEM) and phase-plate TEM (P-TEM) that enables direct observations of the structure of biological molecules in aqueous solution. It is clearly demonstrated that the biological molecules in a water layer can be imaged by the combined method without any stain. The spatial resolution obtained in the present study was about 10nm. This should be improved by using energy filtering. The image contrast of the specimen in water was reduced in comparison with that in vacuum. A model calculation that includes the effects of beam broadening, intensity decrease, and background increase caused by scattering from the water layer around the specimen shows that an increase in the thickness of the water layer reduces the contrast, intensity, and resolution of the image.

Zernike phase contrast cryo-electron tomography of whole mounted frozen cells.

Cryo-electron tomography of frozen hydrated cells has provided cell biologists with an indispensable tool for delineating three-dimensional arrangements of cellular ultrastructure. To avoid the damage induced by electron irradiation, images of frozen hydrated biological specimens are generally acquired under low-dose conditions, resulting in weakly contrasted images that are difficult to interpret, and in which ultrastructural details remain ambiguous. Zernike phase contrast transmission electron microscopy can improve contrast, and can also fix a fatal problem related to the inherent low contrast of conventional electron microscopy, namely, image modulation due to the unavoidable setting of deep defocus. In this study, we applied cryo-electron tomography enhanced with a Zernike phase plate, which avoids image modulation by allowing in-focus setting. The Zernike phase contrast cryo-electron tomography has a potential to suppress grainy background generation. Due to the smoother background in comparison with defocus phase contrast cryo-electron tomography, Zernike phase contrast cryo-electron tomography could yield higher visibility for particulate or filamentous ultrastructure inside the cells, and allowed us to clearly recognize membrane protein structures.

Another 60 years in electron microscopy: development of phase-plate electron microscopy and biological applications.

It has been six decades since the concept of phase-plate electron microscopy was first reported by Boersch, but an experimental report on a phase plate with a theoretically rational performance has only recently been released by a group including the present author. Currently, many laboratories around the world are attempting to develop a wide range of phase plates to enhance the capabilities of transmission electron microscopy. They are reporting not only advantages of their own developments but also a fundamental problem inherent to electron beam devices, namely charging, i.e. the accumulation of electrostatic charge. In this report, we review the 60-year history of phase-plate development, with a particular focus on the fundamental issue of phase-plate charging. Next, we review biological applications of qualified phase plates, which have been successful in avoiding charging to some extent. Finally, we compare and discuss electron microscopic images, taken with or without phase plates, of biological targets such as proteins (GroEL and TRPV4), protein complexes (flagellar motor), viruses (T4 phage, ε-15 phage and herpes simplex virus), bacterial (cyanobacteria) and mammalian (PtK2) cells.

Optimizing the phase shift and the cut-on periodicity of phase plates for TEM.

Images acquired with a phase plate often exhibit fringing and/or contrast reversal artifacts. The two basic parameters controlling the performance of the phase plate are phase shift and cut-on periodicity. We investigate theoretically and numerically the effect of these parameters on the image quality. The analysis covers not just the typical negative phase shift phase plates but also positive phase shift ones. The theoretical study derives formulas for calculating the optimal phase plate phase shift and for the maximum achievable contrast with a given specimen. Two figures of merit - fidelity and contrast - were defined and used to quantify the numerical results. Larger cut-on periodicities provide better performance with higher contrast and less artifacts in the images. Both, the theoretical results and the simulations indicate that positive phase shift phase plates generate higher contrast with better linearity and are free from contrast reversal artifacts. However, with such phase plates the amplitude and the phase contrast components are opposed to each other and the simulations show stronger fringing outside of objects. Based on these results it is difficult to predict if and to what extent the positive phase shift phase plates will be advantageous in practice. Two methods for reduction of fringing artifacts were compared-tapered phase plate and low-frequency amplification software filter. Overall the software solution produced better results and is much easier to implement than modifying the hardware of the phase plate to realize the taper.

Systemic delivery of siRNA to tumors using a lipid nanoparticle containing a tumor-specific cleavable PEG-lipid.

Previously, we developed a multifunctional envelope-type nano device (MEND) for efficient delivery of nucleic acids. For tumor delivery of a MEND, PEGylation is a useful method, which confers a longer systemic circulation and tumor accumulation via the enhanced permeability and retention (EPR) effect. However, PEGylation inhibits cellular uptake and subsequent endosomal escape. To overcome this, we developed a PEG-peptide-DOPE (PPD) that is cleaved in a matrix metalloproteinase (MMP)-rich environment. In this study, we report on the systemic delivery of siRNA to tumors by employing a MEND that is modified with PPD (PPD-MEND). An in vitro study revealed that PPD modification accelerated both cellular uptake and endosomal escape, compared to a conventional PEG modified MEND. To balance both systemic stability and efficient activity, PPD-MEND was further co-modified with PEG-DSPE. As a result, the systemic administration of the optimized PPD-MEND resulted in an approximately 70% silencing activity in tumors, compared to non-treatment. Finally, a safety evaluation showed that the PPD-MEND showed no hepatotoxicity and innate immune stimulation. Furthermore, in a DNA microarray analysis in liver and spleen tissue, less gene alternation was found for the PPD-MEND compared to that for the PEG-unmodified MEND due to less accumulation in liver and spleen.