Correlative Super-Resolution Optical and Atomic Force Microscopy Reveals Relationships Between Bacterial Cell Wall Architecture and Synthesis in Bacillus subtilis

Understanding how bacteria grow and divide requires insight into both the molecular-level dynamics of ultrastructure and the chemistry of the constituent components. Atomic force microscopy (AFM) can provide near molecular resolution images of biological systems but typically provides limited chemical information. Conversely, while super-resolution optical microscopy allows localization of particular molecules and chemistries, information on the molecular context is difficult to obtain. Here, we combine these approaches into STORMForce (stochastic optical reconstruction with atomic force microscopy) and the complementary SIMForce (structured illumination with atomic force microscopy), to map the synthesis of the bacterial cell wall structural macromolecule, peptidoglycan, during growth and division in the rod-shaped bacterium Bacillus subtilis. Using "clickable" d-amino acid incorporation, we fluorescently label and spatially localize a short and controlled period of peptidoglycan synthesis and correlate this information with high-resolution AFM of the resulting architecture. During division, septal synthesis occurs across its developing surface, suggesting a two-stage process with incorporation at the leading edge and with considerable in-filling behind. During growth, the elongation of the rod occurs through bands of synthesis, spaced by ∼300 nm, and corresponds to denser regions of the internal cell wall as revealed by AFM. Combining super-resolution optics and AFM can provide insights into the synthesis processes that produce the complex architectures of bacterial structural biopolymers.

An Open-Source Framework for Automated High-Throughput Cell Biology Experiments

Modern data analysis methods, such as optimization algorithms or deep learning have been successfully applied to a number of biotechnological and medical questions. For these methods to be efficient, a large number of high-quality and reproducible experiments needs to be conducted, requiring a high degree of automation. Here, we present an open-source hardware and low-cost framework that allows for automatic high-throughput generation of large amounts of cell biology data. Our design consists of an epifluorescent microscope with automated XY stage for moving a multiwell plate containing cells and a perfusion manifold allowing programmed application of up to eight different solutions. Our system is very flexible and can be adapted easily for individual experimental needs. To demonstrate the utility of the system, we have used it to perform high-throughput Ca2+ imaging and large-scale fluorescent labeling experiments.

The smfBox is an open-source platform for single-molecule FRET

Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET’s broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community.

Broad uptake of smFRET has been hindered by high instrument costs and a lack of open-source hardware and acquisition software. Here, the authors present the smfBox, a cost-effective open-source platform capable of measuring precise FRET efficiencies between dyes on freely diffusing single molecules.

Molecular coordination of Staphylococcus aureus cell division

The bacterial cell wall is essential for viability, but despite its ability to withstand internal turgor must remain dynamic to permit growth and division. Peptidoglycan is the major cell wall structural polymer, whose synthesis requires multiple interacting components. The human pathogen Staphylococcus aureus is a prolate spheroid that divides in three orthogonal planes. Here, we have integrated cellular morphology during division with molecular level resolution imaging of peptidoglycan synthesis and the components responsible. Synthesis occurs across the developing septal surface in a diffuse pattern, a necessity of the observed septal geometry, that is matched by variegated division component distribution. Synthesis continues after septal annulus completion, where the core division component FtsZ remains. The novel molecular level information requires re-evaluation of the growth and division processes leading to a new conceptual model, whereby the cell cycle is expedited by a set of functionally connected but not regularly distributed components.

Multimodal Super-resolution Optical Microscopy Using a Transition-Metal-Based Probe Provides Unprecedented Capabilities for Imaging Both Nuclear Chromatin and Mitochondria

Detailed studies on the live cell uptake properties of a dinuclear membrane-permeable Ru^II cell probe show that, at low concentrations, the complex localizes and images mitochondria. At concentrations above ∼20 μM, the complex images nuclear DNA. Because the complex is extremely photostable, has a large Stokes shift, and displays intrinsic subcellular targeting, its compatibility with super-resolution techniques was investigated. It was found to be very well suited to image mitochondria and nuclear chromatin in two color, 2C-SIM, and STED and 3D-STED, both in fixed and live cells. In particular, due to its vastly improved photostability compared to that of conventional SR probes, it can provide images of nuclear DNA at unprecedented resolution.

Optical changes induced in Zn porphyrin solutions and LB films by exposure to amines

The 5,10,15,20-tetrakis[3,4-bis(2-ethylhexyloxy)phenyl]-21 H ,23 H -porphinato zinc(II) ( ZnEHO ) is highly stable and exhibits a colorful absorption spectrum in the visible range. Exposure of a chloroform solution of ZnEHO to amines is shown to induce changes in the characteristic optical spectrum owing to charge transfer between the amine and the delocalized π-electron system within the highly conjugated molecule. Solid state Langmuir Blodgett (LB) films containing only ZnEHO are compared to films containing a mixture of ZnEHO and calix[8]arene. The transparent calix[8]arene does not change the optical response but aids the diffusion of the amine gas into the LB films. Atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM) images demonstrate the topological and compositional differences between the samples. The response of the LB films of ZnEHO and calix[8]arene to a variety of different amines demonstrates that this is a good material system for use as an amine sensor.

Combining nanoscale manipulation with macroscale relocation of single quantum dots

We have controllably positioned, with nanometre precision, single CdSe quantum dots referenced to a registration template such that the location of a given nanoparticle on a macroscopic (≈1 cm(2)) sample surface can be repeatedly revisited. The atomically flat sapphire substrate we use is particularly suited to optical measurements of the isolated quantum dots, enabling combined manipulation-spectroscopy experiments on a single particle. Automated nanoparticle manipulation and imaging routines have been developed so as to facilitate the rapid assembly of specific nanoparticle arrangements.

Mapping the fluorescence decay lifetime of a conjugated polymer in a phase-separated blend using a scanning near-field optical microscope

We have studied a blend of the polymers poly(9,9-dioctylfluorene) (F8) dispersed in an inert matrix of polystyrene (PS) using time-resolved scanning near-field optical microscopy (SNOM). On spin-casting, phase separation occurs between the two polymers resulting in a thin film characterized by an F8-rich phase and a PS-rich phase. By spatially mapping the intensity of photoluminescence from the film, we find that there is a low concentration of F8 trapped within the PS-rich phase. We find that the fluorescence emission lifetime (measured at 440 nm) of F8 trapped within the PS-rich phase is significantly longer than that from the F8-rich phase (290 ps compared to 235 ps). Furthermore, spectral measurements indicate that the F8 emission from the PS-rich phase is characterized by a reduced fraction of emission from fluorenone defect states. Taken together, our measurements suggest that in the PS-rich phase interchain exciton diffusion between F8 molecules is suppressed significantly by the effect of dilution.

Responsive brushes and gels as components of soft nanotechnology

Progress in the development of generic molecular devices based on responsive polymers is discussed. Characterisation of specially synthesised polyelectrolyte gels, "grafted from" brushes and triblock copolymers is reported. A Landolt pH-oscillator, based on bromate/ sulfite/ferrocyanide, with a room temperature period of 20 min and a range of 3.1 < pH < 7.0, has been used to drive periodic oscillations in volume in a pH responsive hydrogel. The gel is coupled to the reaction and changes volume by a factor of at least 6. A continuously stirred, constant volume, tank reactor was set-up on an optical microscope and the reaction pH and gel size monitored. The cyclic force generation of this system has been measured directly in a modified JKR experiment. The responsive nature of polyelectrolyte brushes, grown by surface initiated ATRP, have been characterised by scanning force microscopy, neutron reflectometry and single molecule force measurements. Triblock copolymers, based on hydrophobic end-blocks and either polyacid or polybase mid-block, have been used to produce polymer gels where the deformation of the molecules can be followed directly by SAXS and a correlation between molecular shape change and macroscopic deformation has been established. The three systems studied allow both the macroscopic and a molecular response to be investigated independently for the crosslinked gels and the brushes. The triblock copolymers demonstrate that the individual response of the polyelectrolyte molecules scale-up to give the macroscopic response of the system in an oscillating chemical reaction.