Impact of covalent functionalization by diazonium chemistry on the electronic properties of graphene on SiC

Plenty of strategies focused on covalent interaction have been developed to functionalize graphene's surface in order to employ it in a wide range of applications. Among them, the use of radical species including nitrene, carbene and aryl diazonium salts is regarded as a promising strategy to establish the covalent functionalization of graphene. In this work, we highlight the effect of diazonium chemistry on the electronic properties of graphene on SiC. On the basis of X-ray and synchrotron-based photoemission experiments, we were able to prove that 3,4,5-trimethoxybenzenediazonium (TMeOD) units, reduced and chemisorbed onto graphene using electrochemistry, preserve the electronic structure of the Dirac cone, through inducing a slightly additional n-type doping of graphene, as revealed by a downshift of the Dirac cone probed by angle-resolved photoemission experiments.

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.

Bacterial ageing in the absence of external stressors

Evidence of ageing in the bacterium Escherichia coli was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in E. coli in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the 'maternal old pole' progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context. This article is part of a discussion meeting issue 'Single cell ecology'.

Single cell ecology

Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue 'Single cell ecology'.

Single Cell Imaging of Nuclear Architecture Changes

The dynamic architecture of chromatin, the macromolecular complex comprised primarily of DNA and histones, is vital for eukaryotic cell growth. Chemical and conformational changes to chromatin are important markers of functional and developmental processes in cells. However, chromatin architecture regulation has not yet been fully elucidated. Therefore, novel approaches to assessing chromatin changes at the single-cell level are required. Here we report the use of FTIR imaging and microfluidic cell-stretcher chips to assess changes to chromatin architecture and its effect on the mechanical properties of the nucleus in immune cells. FTIR imaging enables label-free chemical imaging with subcellular resolution. By optimizing the FTIR methodology and coupling it with cell segmentation analysis approach, we have identified key spectral changes corresponding to changes in DNA levels and chromatin conformation at the single cell level. By further manipulating live single cells using pressure-driven microfluidics, we found that chromatin decondensation - either during general transcriptional activation or during specific immune cell maturation - can ultimately lead to nuclear auxeticity which is a new biological phenomenon recently identified. Taken together our findings demonstrate the tight and, potentially bilateral, link between extra-cellular mechanotransduction and intra-cellular nuclear architecture.

MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine

Live-cell imaging in microfluidic devices now allows the investigation of cellular heterogeneity within microbial populations. In particular, the mother machine technology developed by Wang et al. has been widely employed to investigate single-cell physiological parameters including gene expression, growth rate, mutagenesis, and response to antibiotics. One of the advantages of the mother machine technology is the ability to generate vast amounts of images; however, the time consuming analysis of these images constitutes a severe bottleneck. Here we overcome this limitation by introducing MMHelper ( https://doi.org/10.5281/zenodo.3254394 ), a publicly available custom software implemented in Python which allows the automated analysis of brightfield or phase contrast, and any associated fluorescence, images of bacteria confined in the mother machine. We show that cell data extracted via MMHelper from tens of thousands of individual cells imaged in brightfield are consistent with results obtained via semi-automated image analysis based on ImageJ. Furthermore, we benchmark our software capability in processing phase contrast images from other laboratories against other publicly available software. We demonstrate that MMHelper has over 90% detection efficiency for brightfield and phase contrast images and provides a new open-source platform for the extraction of single-bacterium data, including cell length, area, and fluorescence intensity.

The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli

Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.

Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy

Background

Clonal microbial populations often harbor rare phenotypic variants that are typically hidden within the majority of the remaining cells, but are crucial for the population’s resilience to external perturbations. Persister and viable but non-culturable (VBNC) cells are two important clonal bacterial subpopulations that can survive antibiotic treatment. Both persister and VBNC cells pose a serious threat to human health. However, unlike persister cells, which quickly resume growth following drug removal, VBNC cells can remain non-growing for prolonged periods of time, thus eluding detection via traditional microbiological assays. Therefore, understanding the molecular mechanisms underlying the formation of VBNC cells requires the characterization of the clonal population with single-cell resolution. A combination of microfluidics, time-lapse microscopy, and fluorescent reporter strains offers the perfect platform for investigating individual cells while manipulating their environment.

Methods

Here, we report a novel single-cell approach to investigate VBNC cells. We perform drug treatment, bacterial culturing, and live/dead staining in series by using transcriptional reporter strains and novel adaptations to the mother machine technology. Since we track each cell throughout the experiment, we are able to quantify the size, morphology and fluorescence that each VBNC cell displayed before, during and after drug treatment.

Results

We show that VBNC cells are not dead or dying cells but share similar phenotypic features with persister cells, suggesting a link between these two subpopulations, at least in the Escherichia coli strain under investigation. We strengthen this link by demonstrating that, before drug treatment, both persister and VBNC cells can be distinguished from the remainder of the population by their lower fluorescence when using a reporter strain for tnaC, encoding the leader peptide of the tnaCAB operon responsible for tryptophan metabolism.

Conclusion

Our data demonstrates the suitability of our approach for studying the physiology of non-growing cells in response to external perturbations. Our approach will allow the identification of novel biomarkers for the isolation of VBNC and persister cells and will open new opportunities to map the detailed biochemical makeup of these clonal subpopulations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0465-4) contains supplementary material, which is available to authorized users.

Particle transport across a channel via an oscillating potential

Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we study particle transport through a channel coupled with an energy well that oscillates its position between the two entrances of the channel. We optimize particle transport across the channel by adjusting the oscillation frequency. At the optimal oscillation frequency, the translocation rate through the channel is a hundred times higher with respect to free diffusion across the channel. Our findings reveal the effect of time-dependent potentials on particle transport across a channel and will be relevant for membrane transport and microfluidics application.

Humidity-enhanced sub-ppm sensitivity to ammonia of covalently functionalized single-wall carbon nanotube bundle layers

A low-cost method for carbon nanotubes (CNTs) network production from solutions on flexible polyethylene naphthalate substrates has been adopted to prepare high quality and well characterized SWCNT bundle layers to be used as the active layer in chemiresistor gas sensors. Two types of SWCNTs have been tested: pristine SWCNTs, deposited from a surfactant solution, and covalently functionalized SWCNTs, deposited from a dimethyl-acetamide solution. The humidity effects on the sensitivity of the SWCNTs network to NH₃ have been investigated. The results show that relative humidity favors the response to NH₃, confirming recent theoretical predictions. The COOH-functionalized sample displays the largest response owing to both its hydrophilic nature, favoring the interaction with H₂O molecules, and its largest surface area. Compared to data available in the literature, the present sensors display a remarkable sensitivity well below the ppm range, which makes them quite promising for environmental and medical applications, where NH₃ concentrations (mostly of the order of tens of ppb) have to be detected.

A cross-functional nanostructured platform based on carbon nanotube-Si hybrid junctions: where photon harvesting meets gas sensing

A combination of the functionalities of carbon nanotube (CNT)-Si hybrid heterojunctions is presented as a novel method to steer the efficiency of the photovoltaic (PV) cell based on these junctions, and to increase the selectivity and sensitivity of the chemiresistor gas sensor operated with the p-doped CNT layer. The electrical characteristics of the junctions have been tracked by exposing the devices to oxidizing (NO2) and reducing (NH3) molecules. It is shown that when used as PV cells, the cell efficiency can be reversibly steered by gas adsorption, providing a tool to selectively dope the p-type layer through molecular adsorption. Tracking of the current-voltage curve upon gas exposure also allowed to use these cells as gas sensors with an enhanced sensitivity as compared to that provided by a readout of the electrical signal from the CNT layer alone. In turn, the chemiresistive response was improved, both in terms of selectivity and sensitivity, by operating the system under illumination, as the photo-induced charges at the junction increase the p-doping of CNTs making them more sensitive to NH3 and less to NO2.

A microfluidic device for characterizing nuclear deformations

Cell nuclei experience and respond to a wide range of forces, both in vivo and in vitro. In order to characterize the nuclear response to physical stress, we developed a microfluidic chip and used it to apply mechanical stress to live cells and measure their nuclear deformability. The device design is optimized for the detection of both nucleus and cytoplasm, which can then be conveniently quantified using a custom-written Matlab program. We measured nuclear sizes and strains of embryonic stem cells, for which we observed negative Poisson ratios in the nuclei. In addition, we were able to detect changes in the nuclear response after treatment with actin depolymerizing and chromatin decondensing agents. Finally, we showed that the device can be used for biologically relevant high-resolution confocal imaging of cells under compression. Thus, the device presented here allows for accurate physical phenotyping at high throughput and has the potential to be applied to a range of cell types.

Gas sensing at the nanoscale: engineering SWCNT-ITO nano-heterojunctions for the selective detection of NH3 and NO2 target molecules

The gas response of single-wall carbon nanotubes (SWCNT) functionalized with indium tin oxide (ITO) nanoparticles (NP) has been studied at room temperature and an enhanced sensitivity to ammonia and nitrogen dioxide is demonstrated. The higher sensitivity in the functionalized sample is related to the creation of nano-heterojunctions at the interface between SWCNT bundles and ITO NP. Furthermore, the different response of the two devices upon NO₂ exposure provides a way to enhance also the selectivity. This behavior is rationalized by considering a gas sensing mechanism based on the build-up of space-charge layers at the junctions. Finally, full recovery of the signal after exposure to NO₂ is achieved by UV irradiation for the functionalized sample, where the ITO NP can play a role to hinder the poisoning effects on SWCNT due to NO₂ chemisorption.

Single-File Escape of Colloidal Particles from Microfluidic Channels

Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount to quantify the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy, and theoretical analysis we uncover the self-similar character of the escape process and provide closed-formula evaluations of the escape time. We find that the escape time scales inversely with the diffusion coefficient of the last particle to leave the channel. Importantly, we find that at the investigated microscale, bias forces as tiny as 10^{-15}  N determine the magnitude of the escape time by drastically reducing interparticle collisions. Our findings provide crucial guidelines to optimize the design of micro- and nanodevices for a variety of applications including drug delivery, particle filtering, and transport in geometrical constrictions.

Ultrafast dynamics in unaligned MWCNTs decorated with metal nanoparticles

The relaxation dynamics of unaligned multi-walled carbon nanotubes decorated with metallic nanoparticles have been studied by using transient optical measurements. The fast dynamics due to the short-lived free-charge carriers excited by the pump are not affected by the presence of nanoparticles. Conversely, a second long dynamics, absent in bare carbon nanotubes, appears only in the decorated samples. A combination of experiment and theory allows us to ascribe this long dynamics to relaxation channels involving electronic states localized at the tube-nanoparticle interface.

Rashba Spin-Orbit Coupling in Image Potential States

The search in two-dimensional condensed matter systems of Rashba-type spin-polarized electronic states is aimed by the possibility to control and manipulate the spin orientation. In this Letter, for the first time, we report on the experimental evidence of a Rashba-type spin splitting in the n=1 image potential state. The image potential state Rashba splitting here measured at the graphene/Ir(111) interface, as confirmed by theoretical considerations, can be detectable to any metal surface with a significant spin-orbit coupling.

Nondecaying Hydrodynamic Interactions along Narrow Channels

Particle-particle interactions are of paramount importance in every multibody system as they determine the collective behavior and coupling strength. Many well-known interactions such as electrostatic, van der Waals, or screened Coulomb interactions, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here we confine two particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance independent in these channels. This finding is of fundamental importance for the interpretation of experiments where dense mixtures of particles or molecules diffuse through finite length, water-filled channels or pore networks.

Steering the efficiency of carbon nanotube-silicon photovoltaic cells by acid vapor exposure: a real-time spectroscopic tracking

Hybrid carbon nanotube-silicon (CNT-Si) junctions have been investigated by angle resolved photoemission spectroscopy (AR-XPS) with the aim to clarify the effects of a nonstoichiometric silicon oxide buried interface on the overall cell efficiency. A complex silicon oxide interface has been clearly identified and its origin and role in the heterojunction have been probed by exposing the cells to hydrofluoric (HF) and nitric (HNO3) acid. Real-time monitoring of the cell efficiencies during the steps following acid exposure (up to 1 week after etching) revealed a correlation between the thickness and chemical state of the oxide layer and the cell efficiencies. By matching the AR-XPS and Raman spectroscopy with the electrical response data it has been possible to discriminate the effects on the cell efficiency of the buried SiO(x) interface from those related to CNT acid doping. The overall cell behavior recorded for different thicknesses of the SiO(x) interface indicates that the buried oxide layer is likely acting as a passivating/inversion layer in a metal-insulator-semiconductor junction.

Channel-facilitated diffusion boosted by particle binding at the channel entrance

We investigate single-file diffusion of Brownian particles in arrays of closely confining microchannels permeated by a variety of attractive optical potentials and connecting two baths with equal particle concentration. We simultaneously test free diffusion in the channel, diffusion in optical traps coupled in the center of the channel, and diffusion in traps extending into the baths. We found that both classes of attractive optical potentials enhance the translocation rate through the channel with respect to free diffusion. Surprisingly, for the latter class of potentials we measure a 40-fold enhancement in the translocation rate with respect to free diffusion and find a sublinear power law dependence of the translocation rate on the average number of particles in the channel. Our results reveal the function of particle binding at the channel entrances for diffusive transport and open the way to a better understanding of membrane transport and design of synthetic membranes with enhanced diffusion rate.

A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes

With the rise in antibiotic resistance amongst pathogenic bacteria, the study of antibiotic activity and transport across cell membranes is gaining widespread importance. We present a novel, label-free microfluidic assay that quantifies the permeability coefficient of a broad spectrum fluoroquinolone antibiotic, norfloxacin, across lipid membranes using the UV autofluorescence of the drug. We use giant lipid vesicles as highly controlled model systems to study the diffusion through lipid membranes. Our technique directly determines the permeability coefficient without requiring the measurement of the partition coefficient of the antibiotic.

Selective transport control on molecular velcro made from intrinsically disordered proteins

The selectivity and speed of many biological transport processes transpire from a 'reduction of dimensionality' that confines diffusion to one or two dimensions instead of three. This behaviour remains highly sought after on polymeric surfaces as a means to expedite diffusional search processes in molecular engineered systems. Here, we have reconstituted the two-dimensional diffusion of colloidal particles on a molecular brush surface. The surface is composed of phenylalanine-glycine nucleoporins (FG Nups)--intrinsically disordered proteins that facilitate selective transport through nuclear pore complexes in eukaryotic cells. Local and ensemble-level experiments involving optical trapping using a photonic force microscope and particle tracking by video microscopy, respectively, reveal that 1-µm-sized colloidal particles bearing nuclear transport receptors called karyopherins can exhibit behaviour that varies from highly localized to unhindered two-dimensional diffusion. Particle diffusivity is controlled by varying the amount of free karyopherins in solution, which modulates the multivalency of Kap-binding sites within the molecular brush. We conclude that the FG Nups resemble stimuli-responsive molecular 'velcro', which can impart 'reduction of dimensionality' as a means of biomimetic transport control in artificial environments.