Metal nanoparticles are used as catalysts in a variety of important chemical reactions, and can have a range of different shapes, with facets and sites that differ in catalytic reactivity. To develop better catalysts it is necessary to determine where catalysis occurs on such nanoparticles and what structures are more reactive. Surface science experiments or theory can be used to predict the reactivity of surfaces with a known structure, and the reactivity of nanocatalysts can often be rationalized from a knowledge of their well-defined surface facets. Here, we show that a knowledge of the surface facets of a gold nanorod catalyst is insufficient to predict its reactivity, and we must also consider defects on the surface of the nanorod. We use super-resolution fluorescence microscopy to quantify the catalysis of the nanorods at a temporal resolution of a single catalytic reaction and a spatial resolution of ∼40 nm. We find that within the same surface facets on the sides of a single nanorod, the reactivity is not constant and exhibits a gradient from the centre of the nanorod towards its two ends. Furthermore, the ratio of the reactivity at the ends of the nanorod to the reactivity at the sides varies significantly from nanorod to nanorod, even though they all have the same surface facets.

One of the hallmarks of opportunistic pathogens is their ability to adjust and respond to a wide range of environmental and host-associated conditions. The human pathogen Pseudomonas aeruginosa has an ability to thrive in a variety of hosts and cause a range of acute and chronic infections in individuals with impaired host defenses or cystic fibrosis. Here we report an in-depth transcriptional profiling of this organism when grown at host-related temperatures. Using RNA-seq of samples from P. aeruginosa grown at 28°C and 37°C we detected genes preferentially expressed at the body temperature of mammalian hosts, suggesting that they play a role during infection. These temperature-induced genes included the type III secretion system (T3SS) genes and effectors, as well as the genes responsible for phenazines biosynthesis. Using genome-wide transcription start site (TSS) mapping by RNA-seq we were able to accurately define the promoters and cis-acting RNA elements of many genes, and uncovered new genes and previously unrecognized non-coding RNAs directly controlled by the LasR quorum sensing regulator. Overall we identified 165 small RNAs and over 380 cis-antisense RNAs, some of which predicted to perform regulatory functions, and found that non-coding RNAs are preferentially localized in pathogenicity islands and horizontally transferred regions. Our work identifies regulatory features of P. aeruginosa genes whose products play a role in environmental adaption during infection and provides a reference transcriptional landscape for this pathogen.

This review discusses the latest advances in using single-molecule microscopy of fluorogenic reactions to examine and understand the spatiotemporal catalytic behaviors of single metal nanoparticles of various shapes including pseudospheres, nanorods, and nanoplates. Real-time single-turnover kinetics reveal size-, catalysis-, and metal-dependent temporal activity fluctuations of single pseudospherical nanoparticles (<20 nm in diameter). These temporal catalytic dynamics can be related to nanoparticles' dynamic surface restructuring whose timescales and energetics can be quantified. Single-molecule super-resolution catalysis imaging further enables the direct quantification of catalytic activities at different surface sites (i.e., ends vs. sides, or corner, edge vs. facet regions) on single pseudo 1-D and 2-D nanocrystals, and uncovers linear and radial activity gradients within the same surface facets. These spatial activity patterns within single nanocrystals can be attributed to the inhomogeneous distributions of low-coordination surface sites, including corner, edge, and defect sites, among which the distribution of defect sites is correlated with the nanocrystals' morphology and growth mechanisms. A brief discussion is given on the extension of the single-molecule imaging approach to catalysis that does not involve fluorescent molecules.

Summary During environmental adaptation bacteria use small regulatory RNAs (sRNAs) to repress or activate expression of a large fraction of their proteome. We extended the use of the in vivo RNA proximity ligation method towards probing global sRNA interactions with their targets in Pseudomonas aeruginosa and verified the method with a known regulon controlled by the PrrF1 sRNA. We also identified two sRNAs (Sr0161 and ErsA) that interact with the mRNA encoding the major porin OprD responsible for the uptake of carbapenem antibiotics. These two sRNAs base pair with the 5′ UTR of oprD leading to increase in resistance of the bacteria to meropenem. Additional proximity ligation experiments and enrichment for Sr0161 targets identified the mRNA for the regulator of type III secretion system. Interaction between the exsA mRNA and Sr0161 leads to a block in the synthesis of a component of the T3SS apparatus and an effector. Another sRNA, Sr006, positively regulates, without Hfq, the expression of PagL, an enzyme responsible for deacylation of lipid A, reducing its pro-inflammatory property and resulting in polymyxin resistance. Therefore, an analysis of global sRNA-mRNA interactions can lead to discoveries of novel pathways controlling gene expression that are likely integrated into larger regulatory networks.

This tutorial review covers recent developments in using single-molecule fluorescence microscopy to study nanoscale catalysis. The single-molecule approach enables following catalytic and electrocatalytic reactions on nanocatalysts, including metal nanoparticles and carbon nanotubes, at single-reaction temporal resolution and nanometer spatial precision. Real-time, in situ, multiplexed measurements are readily achievable under ambient solution conditions. These studies provide unprecedented insights into catalytic mechanism, reactivity, selectivity, and dynamics in spite of the inhomogeneity and temporal variations of catalyst structures. Prospects, generality, and limitations of the single-molecule fluorescence approach for studying nanocatalysis are also discussed.