CREIM: Coffee Ring Effect Imaging Model for Monitoring Protein Self-Assembly in Situ

An Efficiently Doped PEDOT:PSS Ink Formulation via Metastable Liquid-Liquid Contact for Capillary Flow-Driven, Hierarchically and Highly Conductive Films

With commercial electronics transitioning toward flexible devices, there is a growing demand for high-performance polymers such as poly(3,4-ethylenedioxythiophene): poly(styrene sulfonate) (PEDOT:PSS). Previous breakthroughs in promoting the conductivity of PEDOT:PSS, which mainly stem from solvent-treatment and transfer-printing strategies, remain as inevitable challenges due to the inefficient, unstable, and biologically incompatible process. Herein, a scalable fabrication of conducting PEDOT:PSS inks is reported via a metastable liquid-liquid contact (MLLC) method, realizing phase separation and removal of excess PSS simultaneously. MLLC-doped inks are further used to prepare ring-like films through a compromise between the coffee-ring effect and the Marangoni vortex during evaporation of droplets. The specific control over deposition conditions allows for tunable ring-like morphologies and preferentially interconnected networks of PEDOT:PSS nanofibrils, resulting in a high electrical conductivity of 6,616 S cm^-1 and excellent optical transparency of the film. The combination of excellent electrical properties and the special morphology enables it to serve as electrodes for touch sensors with gradient pressure sensitivity. These findings not only provide new insight into developing a simple and efficient doping method for commercial PEDOT:PSS ink, but also offer a promising self-assembled deposition pattern of organic semiconductor films, expanding the applications in flexible electronics, bioelectronics as well as photovoltaic devices.

Super-resolution structured illumination microscopy: past, present and future

Structured illumination microscopy (SIM) has emerged as an essential technique for three-dimensional (3D) and live-cell super-resolution imaging. However, to date, there has not been a dedicated workshop or journal issue covering the various aspects of SIM, from bespoke hardware and software development and the use of commercial instruments to biological applications. This special issue aims to recap recent developments as well as outline future trends. In addition to SIM, we cover related topics such as complementary super-resolution microscopy techniques, computational imaging, visualization and image processing methods. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.

mmSIM: an open toolbox for accessible structured illumination microscopy

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.

Visualization Method for the Cell-Level Vesicle Transport Using Optical Flow and a Diverging Colormap

Elucidation of cell-level transport mediated by vesicles within a living cell provides key information regarding viral infection processes and also drug delivery mechanisms. Although the single-particle tracking method has enabled clear analysis of individual vesicle trajectories, information regarding the entire cell-level intracellular transport is hardly obtainable, due to the difficulty in collecting a large dataset with current methods. In this paper, we propose a visualization method of vesicle transport using optical flow, based on geometric cell center estimation and vector analysis, for measuring the trafficking directions. As a quantitative visualization method for determining the intracellular transport status, the proposed method is expected to be universally exploited in various biomedical cell image analyses.

A Mechanistic Model for Bacterial Retention and Infiltration on a Leaf Surface during a Sessile Droplet Evaporation

Evaporation of sessile droplets on the surface of plant leaves is a process that frequently occurs during plant growth as well as postharvest processes. Evaporation-driven internal flows within sessile droplets can transport microorganisms near the leaf surface, facilitating their adhesion to surface microstructures such as trichomes, and infiltration into available openings such as stomata and grooves. A mechanistic model for this retention and infiltration pathway was developed. Solution domain is a sessile droplet located on a leaf surface, as well as its surrounding gas. The model includes fluid flow within the droplet and gas phases, gas-water interface tracking, heat transfer, transport of vapor in gas, and transport of sugar and bacteria within water. The model results are validated based on available literature data and experimental images. The results showed that a hydrophilic surface would promote bacterial retention and infiltration. Evaporation-driven flows increase concentration of bacteria around or inside microstructures at the leaf surface, facilitating their adhesion and infiltration. Larger microstructures having wider spacing between them increased the retention. A higher evaporation rate led to higher infiltration. Chemotaxis toward nutrients at the leaf surface and random motility were shown to decrease the retention and infiltration during evaporation.

Monitoring the Assembly and Aggregation of Polypeptide Materials by Time-Resolved Emission Spectra

Polypeptide assembly and aggregation are the common forms of its physiological and pathological activity, and monitoring them on a molecular level is critical for resolving numerous medical (e.g., onset of neurodegenerative diseases) or biological problems. Sensitivity of the intrinsic fluorescence of protein to its assembly, aggregation, or complexation offers a noninvasive methodology for identifying and determining different stages of these processes. In this protocol, we present the approach based on the time-resolved emission spectra (TRES), which reveals the number of fluorescent residues, the presence of dielectric relaxation, and the changes in fluorescence kinetics during aggregation.

Marangoni flows drive the alignment of fibrillar cell-laden hydrogels

When a sessile droplet containing a solute in a volatile solvent evaporates, flow in the droplet can transport and assemble solute particles into complex patterns. Transport in evaporating sessile droplets has largely been examined in solvents that undergo complete evaporation. Here, we demonstrate that flow in evaporating aqueous sessile droplets containing type I collagen-a self-assembling polymer-can be harnessed to engineer hydrated networks of aligned collagen fibers. We find that Marangoni flows direct collagen fiber assembly over millimeter-scale areas in a manner that depends on the rate of self-assembly, the relative humidity of the surrounding environment, and the geometry of the droplet. Skeletal muscle cells that are incorporated into and cultured within these evaporating droplets collectively orient and subsequently differentiate into myotubes in response to aligned networks of collagen. Our findings demonstrate a simple, tunable, and high-throughput approach to engineer aligned fibrillar hydrogels and cell-laden biomimetic materials.

Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy

Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.

Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters

Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.