The multifarious MerR family of transcriptional regulators

The MerR family of transcriptional regulators includes a variety of bacterial cytoplasmic proteins that respond to a wide range of signals, including toxins, metal ions, and endogenous metabolites. Its best-characterized members share similar structural and functional features with the family founder, the mercury sensor MerR, although most of them do not respond to metal ions. The group of "canonical" MerR homologs displays common molecular mechanisms for controlling the transcriptional activation of their target genes in response to inducer signals. This includes the recognition of distinctive operator sequences located at suboptimal σ70 -dependent promoters. Interestingly, an increasing number of proteins assigned to the MerR family based on their DNA-binding domain do not match in structure, sequence, or mode of action with any of the canonical MerR-like regulators. Here, we analyzed several members of the family, including this last group. Based on a phylogenetic analysis, and similarities in structural/functional features and position of their target operators relative to the promoter elements, we propose to assign these "atypical/divergent" MerR regulators to a phylogenetically separated group. These atypical/divergent homologs represent a new class of transcriptional regulators with novel regulatory mechanisms.

Ensemble and single-particle level fluorescent fine-tuning of carbon dots via positional changes of amines toward "supervised" oral microbiome sensing

Significance

Carbon dots (CDs) have attracted a host of research interest in recent years mainly due to their unique photoluminescence (PL) properties that make them applicable in various biomedical areas, such as imaging and image-guided therapy. However, the real mechanism underneath the PL is a subject of wide controversy and can be investigated from various angles.

Aim

Our work investigates the effect of the isomeric nitrogen position as the precursor in the synthesis of CDs by shedding light on their photophysical properties on the single particles and ensemble level.

Approach

To this end, we adopted five isomers of diaminopyridine (DAP) and urea as the precursors and obtained CDs during a hydrothermal process. The various photophysical properties were further investigated in depth by mass spectroscopy. CD molecular frontier orbital analyses aided us in justifying the fluorescence emission profile on the bulk level as well as the charge transfer processes. As a result of the varying fluorescent responses, we indicate that these particles can be utilized for machine learning (ML)-driven sensitive detection of oral microbiota. The sensing results were further supported by density functional theoretical calculations and docking studies.

Results

The generating isomers have a significant effect on the overall photophysical properties at the bulk/ensembled level. On the single-particle level, although some of the photophysical properties such as average intensity remained the same, the overall differences in brightness, photo-blinking frequency, and bleaching time between the five samples were conceived. The various photophysical properties could be explained based on the different chromophores formed during the synthesis. Overall, an array of CDs was demonstrated herein to achieve ∼100% separation efficacy in segregating a mixed oral microbiome culture in a rapid (<0.5  h), high-throughput manner with superior accuracy.

Conclusions

We have indicated that the PL properties of CDs can be regulated by the precursors' isomeric position of nitrogen. We emancipated this difference in a rapid method relying on ML algorithms to segregate the dental bacterial species as biosensors.

Patterned Liquid-Infused Nanocoating Integrating a Sensitive Bacterial Sensing Ability to an Antibacterial Surface

The slippery liquid-infused surfaces show a great antibacterial property. However, most liquid-infused surfaces cannot detect whether or not the unknown aqueous samples contain microorganisms. Therefore, it is highly necessary but a challenge to integrate bacterial sensing capability into antibacterial surface. In this work, we prepared a slippery patterned liquid-infused nanocoating on the glass substrate for integrating bacterial sensing capability into the bacterial repellence surface. Dendritic mesoporous silica nanoparticles (DMSNs) with a suitable particle size of ca. 128 nm were employed as a building block to fabricate the multifunctional nanocoating with a superhydrophilic microwell and hydrophobic periphery by a dip-coating strategy, hydrophobic treatment, photomask-mediated plasma etching, and liquid infusion. Dendritic porous silica nanoparticles (DPSNs) with a larger particle size of ca. 260 nm were uniformly loaded with Au nanoparticles (NPs), providing large surface area for the modification of Raman reporter (4-mercaptobenzoic acid (4-MBA)) and aptamer. Thus, as a Raman tag, the formed DPSNs-Au-MBA-aptamer could achieve sensitive surface-enhanced Raman spectroscopy (SERS) detection of target bacteria. Combined with the Raman tag, the patterned liquid-infused nanocoating not only completely repelled bacteria on the hydrophobic area but also enabled sensitive SERS detection of Staphylococcus aureus in a very low sample volume (1 μL) with a low detection limit of 2.6 colony formation units (CFU)/mL on the antibody-modified superhydrophilic microwell. This research provided a novel and reliable strategy to construct a multifunctional nanocoating with microbial repellence and sensing capabilities.

Carbon Dots as an Emergent Class of Antimicrobial Agents

Antimicrobial resistance is a recognized global challenge. Tools for bacterial detection can combat antimicrobial resistance by facilitating evidence-based antibiotic prescribing, thus avoiding their overprescription, which contributes to the spread of resistance. Unfortunately, traditional culture-based identification methods take at least a day, while emerging alternatives are limited by high cost and a requirement for skilled operators. Moreover, photodynamic inactivation of bacteria promoted by photosensitisers could be considered as one of the most promising strategies in the fight against multidrug resistance pathogens. In this context, carbon dots (CDs) have been identified as a promising class of photosensitiser nanomaterials for the specific detection and inactivation of different bacterial species. CDs possess exceptional and tuneable chemical and photoelectric properties that make them excellent candidates for antibacterial theranostic applications, such as great chemical stability, high water solubility, low toxicity and excellent biocompatibility. In this review, we will summarize the most recent advances on the use of CDs as antimicrobial agents, including the most commonly used methodologies for CD and CD/composites syntheses and their antibacterial properties in both in vitro and in vivo models developed in the last 3 years.

Simultaneous Ultrasensitive Detection and Elimination of Drug-Resistant Bacteria by Cyclometalated Iridium(III) Complexes

Antimicrobial resistance has become a major threat to public health due to the rampant and empirical use of antibiotics. Rapid diagnosis of bacteria with the desired sensitivity and selectivity still, however, remains an open challenge. We report a special class of water-soluble metal-based aggregation-induced emission luminogens (AIEgens), namely, cyclometalated iridium(III) polypyridine complexes of the type [Ir(PQ)₂(N^N)]Cl (1-3), where PQ = 2-phenylquinoline and N^N = 2,2'-bipyridine derivatives, that demonstrate dual capability for detection and elimination of drug-resistant bacteria in aqueous solutions. These AIEgens exhibit selective and rapid sensing of endotoxins, such as lipopolysaccharides (LPS) and lipoteichoic acid (LTA) released by the bacteria, with a detection limit in the lower nanomolar range. Targeting these naturally amplified biomarkers (approximately 1 million copies per cell) by iridium(III) complexes induces strong AIE in the presence of different Gram-negative and Gram-positive bacteria including carbapenem-resistant A. baumannii (CRAB) and methicillin-resistant S. aureus (MRSA) at concentrations as low as 1.2 CFU/mL within 5 min in spiked water samples. Detection of bacteria by the complexes is also visible to the naked eye at higher (10⁸ CFU/mL) cell concentrations. More notably, complexes 1 and 2 show potent antibacterial activity against drug-resistant bacteria with low minimum inhibitory concentrations (MICs) ≤ 5 μg/mL (1-4 μM) via ROS generation and cell membrane disintegrity. To the best of our knowledge, this work is the "first-in-class" example of a metal-based theranostic system that integrates selective, sensitive, rapid, naked-eye, wash-free, and real-time detection of bacteria using broad-spectrum antibiotics into a single platform. This dual capability of AIEgens makes them ideal scaffolds for monitoring bacterial contamination in aqueous samples and pharmaceutical applications.

Bacterial Sensing and Biofilm Monitoring for Infection Diagnostics

Recent insights into the rapidly emerging field of bacterial sensing and biofilm monitoring for infection diagnostics are discussed as well as recent key developments and emerging technologies in the field. Electrochemical sensing of bacteria and bacterial biofilm via synthetic, natural, and engineered recognition, as well as direct redox-sensing approaches via algorithm-based optical sensing, and tailor-made optotracing technology are discussed. These technologies are highlighted to answer the very critical question: "how can fast and accurate bacterial sensing and biofilm monitoring be achieved? Following on from that: "how can these different sensing concepts be translated for use in infection diagnostics? A central obstacle to this transformation is the absence of direct and fast analysis methods that provide high-throughput results and bio-interfaces that can control and regulate the means of communication between biological and electronic systems. Here, the overall progress made to date in building such translational efforts at the level of an individual bacterial cell to a bacterial community is discussed.

Conjugated Oligo- and Polymers for Bacterial Sensing

Fast and accurate detection of bacteria and differentiation between pathogenic and commensal colonization are important keys in preventing the emergence and spread of bacterial resistance toward antibiotics. As bacteria undergo major lifestyle changes during colonization, bacterial sensing needs to be achieved on different levels. In this review, we describe how conjugated oligo- and polymers are used to detect bacterial colonization. We summarize how oligothiophene derivatives have been tailor-made for detection of biopolymers produced by a wide range of bacteria upon entering the biofilm lifestyle. We further describe how these findings are translated into diagnostic approaches for biofilm-related infections. Collectively, this provides an overview on how synthetic biorecognition elements can be used to produce fast and easy diagnostic tools and new methods for infection control.

Plasmonic Nanotrough Networks for Scalable Bacterial Raman Biosensing

We demonstrate a novel approach for fabricating surface enhanced Raman scattering (SERS) substrates for single bacterial biosensing based on Ag cylindrical nanotrough networks (CNNs). This approach is developed with large scalability by leveraging a cellulose nanofiber template fabrication via facile electrospinning. Specifically, a concave nanotrough structure consisting of interconnected concave Ag nanoshells is demonstrated by depositing a thin layer of Ag atop a sacrificial electrospun nanofiber template and then completely removing the cellulose core in water. Our investigations of the scattering properties and SERS performances of single isolated Ag nanotroughs of different diameters reveal that nanotrough-based substrates provide tunable optical responses and enhanced SERS intensities. Further, Ag CNNs are fabricated in highly interconnected networks that yield reproducible SERS signals for molecular monolayers and whole bacterial cells, enabling rapid spectral discrimination between different bacterial strains. Finally, by performing principal component analysis on a large number of measured SERS spectra (40 spectra per bacterium), we demonstrate successful spectral discrimination between two types of Escherichia coli ( E. coli) bacteria, that is, E. coli K12 with its derivative E. coli DH 5α and E. coli BL21(DE3). The demonstrated cost-effective substrates feature several advantages over conventional SERS substrates including environmentally friendly and scalable fabrication compatible with versatile devices and provide an alternative approach to rapid SERS detection and screening of biochemicals.

Real-Time Detection of Staphylococcus Aureus Using Whispering Gallery Mode Optical Microdisks

Whispering Gallery Mode (WGM) microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q) factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 10⁴ is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme.

Prostaglandin pathways in duodenal chemosensing

Acid-sensing pathways, which trigger mucosal defense mechanisms in response to luminal acid, involve the rapid afferent-mediated "capsaicin pathway" and the sustained "prostaglandin (PG) pathway." Luminal acid quickly increases protective PG synthesis and release from epithelia, although the mechanism by which luminal acid induces PG synthesis is still mostly unknown. Acid exposure augments purinergic ATP-P2Y signaling by inhibition of intestinal alkaline phosphatase activity. Since P2Y activation increases intracellular Ca2+, we further hypothesized that ATP-P2Y signals increase the generation of H2O2 derived from dual oxidase, a member of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase family activated by Ca2+. Our recent studies suggest that acid exposure increases H2O2 output, followed by phospholipase A2 and cyclooxygenase activation, increasing PG synthesis. Released prostaglandin E2 augments protective HCO3- and mucus secretion via EP4 receptor activation. Thus, the PG pathway as a component of duodenal acid sensing consists of acid-related intestinal alkaline phosphatase inhibition, ATP-P2Y signals, dual oxidase 2-derived H2O2 production, phospholipase A2 activation, prostaglandin E2 synthesis, and EP4 receptor activation. The PG pathway is also involved in luminal bacterial sensing in the duodenum via activation of pattern recognition receptors, including Toll-like receptors and nucleotide-binding oligomerization domain 2. The presence of acute mucosal responses to luminal bacteria suggests that the duodenum is important for host defenses and may reduce bacterial loading to the hindgut using H2O2, complementing gastric acidity and anti-bacterial bile acids.

Update on biologic pathways in inflammatory bowel disease and their therapeutic relevance

Results of recent genetic and immunologic studies have brought to the forefront several biologic pathways that allow for a better understanding of the mechanisms of tissue homeostasis, on the one hand, and inflammatory bowel disease (IBD) on the other. The explosion of research activity as a result of these newly identified targets is bringing the pathogenesis of these complex disorders into focus as well as creating new therapeutic opportunities. The greatest advances with perhaps the largest impact on our understanding of the etiology of Crohn's disease are those related to bacterial sensing, such as through nucleotide-binding oligomerization domain-containing protein 2 (NOD2) and its relationships to autophagy and the unfolded protein response as a consequence of endoplasmic reticulum stress. Interestingly, it appears as though these pathways, which are rooted in microbial sensing and regulation, are interrelated. Genetic studies have also renewed interest in previously studied pathways in IBD, such as the formation and function of the inflammasome and its relationship to interleukin (IL) 1-beta signaling. With the recent success of therapeutic agents designed to block tumor necrosis factor, the IL-12/23 pathways, and lymphocyte homing, insights have been gained into the biologic relevance and impact of these various inflammatory pathways in IBD. In this review, the exciting recent advances in these biologic pathways of IBD are discussed, particularly in light of their therapeutic relevance.

Electrical detection of pathogenic bacteria via immobilized antimicrobial peptides

The development of a robust and portable biosensor for the detection of pathogenic bacteria could impact areas ranging from water-quality monitoring to testing of pharmaceutical products for bacterial contamination. Of particular interest are detectors that combine the natural specificity of biological recognition with sensitive, label-free sensors providing electronic readout. Evolution has tailored antimicrobial peptides to exhibit broad-spectrum activity against pathogenic bacteria, while retaining a high degree of robustness. Here, we report selective and sensitive detection of infectious agents via electronic detection based on antimicrobial peptide-functionalized microcapacitive electrode arrays. The semiselective antimicrobial peptide magainin I--which occurs naturally on the skin of African clawed frogs--was immobilized on gold microelectrodes via a C-terminal cysteine residue. Significantly, exposing the sensor to various concentrations of pathogenic Escherichia coli revealed detection limits of approximately 1 bacterium/μL, a clinically useful detection range. The peptide-microcapacitive hybrid device was further able to demonstrate both Gram-selective detection as well as interbacterial strain differentiation, while maintaining recognition capabilities toward pathogenic strains of E. coli and Salmonella. Finally, we report a simulated "water-sampling" chip, consisting of a microfluidic flow cell integrated onto the hybrid sensor, which demonstrates real-time on-chip monitoring of the interaction of E. coli cells with the antimicrobial peptides. The combination of robust, evolutionarily tailored peptides with electronic read-out monitoring electrodes may open exciting avenues in both fundamental studies of the interactions of bacteria with antimicrobial peptides, as well as the practical use of these devices as portable pathogen detectors.