Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation.

The severity of T cell-mediated gastrointestinal (GI) diseases such as graft-versus-host disease (GVHD) and inflammatory bowel diseases correlates with a decrease in the diversity of the host gut microbiome composition characterized by loss of obligate anaerobic commensals. The mechanisms underpinning these changes in the microbial structure remain unknown. Here, we show in multiple specific pathogen-free (SPF), gnotobiotic, and germ-free murine models of GI GVHD that the initiation of the intestinal damage by the pathogenic T cells altered ambient oxygen levels in the GI tract and caused dysbiosis. The change in oxygen levels contributed to the severity of intestinal pathology in a host intestinal HIF-1α- and a microbiome-dependent manner. Regulation of intestinal ambient oxygen levels with oral iron chelation mitigated dysbiosis and reduced the severity of the GI GVHD. Thus, targeting ambient intestinal oxygen levels may represent a novel, non-immunosuppressive strategy to mitigate T cell-driven intestinal diseases.

Mix and Match Tuning of the Conformational and Multistate Redox Switching Properties of an Overcrowded Alkene.

Overcrowded alkenes have received considerable attention as versatile structural motifs in a range of optical switches and light-driven unidirectional motors. In contrast, their actuation by electrochemical stimuli remains underexplored, even though this alternative energy input may be preferred in various applications and enables additional control over molecular switching states and properties. While symmetric bistricyclic overcrowded enes (BAEs) containing two identical halves based on either thioxanthene (TX) or acridine (Acr) motifs are known to be reversible conformational redox switches, their redox potentials are generally too high or low, respectively, thereby preventing wider applications. Herein, we demonstrate that the "mixed" TX-Acr switch possesses redox properties that lie between those of its parent symmetric analogs, enabling interconversion between three stable redox and conformational states at mild potentials. This includes the neutral anti-folded, the dicationic orthogonal, and a unique twisted monoradical cation state, the latter of which is only accessible in the case of the mixed TX-Acr switch and in a pathway-dependent manner. Consequently, with this multistate redox switch, a myriad of molecular properties, including geometry, polarity, absorbance, and fluorescence, can be modulated with high fidelity and reversibility between three distinct stable states. More generally, this study highlights the versatility of the "mix and match" approach in rationally designing redox switches with specific (redox) properties, which in turn is expected to enable a myriad of applications ranging from molecular logic and memory to actuators and energy storage systems.

Redox-Switchable Aromaticity in a Helically Extended Indeno[2,1-c]fluorene.

Molecular switches have received major attention to enable the reversible modulation of various molecular properties and have been extensively used as trigger elements in diverse fields, including molecular machines, responsive materials, and photopharmacology. Antiaromaticity is a fascinating property that has attracted not only significant fundamental interest but is also increasingly relevant in different applications, in particular organic (opto)electronics. However, designing systems in which (anti)aromaticity can be judiciously and reversibly switched ON and OFF remains challenging. Herein, we report a helicene featuring an indenofluorene-bridged bisthioxanthylidene as a novel switch wherein a simultaneous two-electron (electro)chemical redox process allows highly reversible modulation of its (anti)aromatic character. Specifically, the two thioxanthylidene rotors, attached to the initially aromatic indenofluorene scaffold via overcrowded alkenes, adopt an anti-folded structure, which upon oxidation convert to singly bonded, twisted conformations. This is not only associated with significant (chir)optical changes but importantly also results in formation of the fully conjugated, formally antiaromatic as-indacene motif in the helical core of the switch. This process proceeds without the buildup of radical cation intermediates and thus enables highly reversible switching of molecular geometry, aromaticity, absorbance, and chiral expression under ambient conditions, as evidenced by NMR, UV-vis, CD, and (spectro)electrochemical analyses, supported by DFT calculations. We expect this concept to be extendable to a wide range of robust antiaromatic-aromatic switches and to provide a basis for modulation of the structure and properties of these fascinating inherently chiral polycyclic π-scaffolds.

Halogen Bonding Tripodal Metallo-Receptors for Phosphate Recognition and Sensing in Aqueous-Containing Organic Media.

The anion recognition and electrochemical anion-sensing properties of halogen-bonding (XB) tripodal zinc(II) receptors strategically designed and constructed for tetrahedral anion guest binding are described. The XB tris(iodotriazole)-containing hosts exhibit high affinities and selectivities for inorganic phosphate over other more basic, mono-charged oxoanions such as acetate and the halides in a competitive CD3 CN/D2 O (9 : 1 v/v) aqueous solvent mixture. 1 H NMR anion binding and electrochemical voltammetric anion sensing studies with redox-active ferrocene functionalised metallo-tripodal receptor analogues, reveal each of the XB tripods as superior anion complexants when compared to their tris(prototriazole)-containing, hydrogen bonding (HB) counterparts, not only exemplifying the halogen bond as a strong alternative interaction to the traditional hydrogen bond for molecular recognition but also providing rare evidence of the ability of XB receptors to preferentially bind the "harder" phosphate oxoanion over the "softer" and less hydrated halides in aqueous containing media.

Anion Sensing through Redox-Modulated Fluorescent Halogen Bonding and Hydrogen Bonding Hosts.

Anion sensing via either optical or electrochemical readouts has separately received enormous attention, however, a judicious combination of the advantages of both modalities remains unexplored. Toward this goal, we herein disclose a series of novel, redox-active, fluorescent, halogen bonding (XB) and hydrogen bonding (HB) BODIPY-based anion sensors, wherein the introduction of a ferrocene motif induces remarkable changes in the fluorescence response. Extensive fluorescence anion titration, lifetime and electrochemical studies reveal anion binding-induced emission modulation through intramolecular photoinduced electron transfer (PET), the magnitude of which is dependent on the nature of both the XB/HB donor and anion. Impressively, the XB sensor outperformed its HB congener in terms of anion binding strength and fluorescence switching magnitude, displaying significant fluorescence turn-OFF upon anion binding. In contrast, redox-inactive control receptors display a turn-ON response, highlighting the pronounced impact of the introduction of the redox-active ferrocene on the optical sensing performance. Additionally, the redox-active ferrocene motif also serves as an electrochemical reporter group, enabling voltammetric anion sensing in competitive solvents. The combined advantages of both sensing modalities were further exploited in a novel, proof-of-principle, fluorescence spectroelectrochemical anion sensing approach, enabling simultaneous and sensitive read out of optical and electrochemical responses in multiple oxidation states and at very low receptor concentration.

A Multiresponsive Ferrocene-Based Chiral Overcrowded Alkene Twisting Liquid Crystals.

The reversible modulation of chirality has gained significant attention not only for fundamental stereochemical studies but also for numerous applications ranging from liquid crystals (LCs) to molecular motors and machines. This requires the construction of switchable molecules with (multiple) chiral elements in a highly enantioselective manner, which is often a significant synthetic challenge. Here, we show that the dimerization of an easily accessible enantiopure planar chiral ferrocene-indanone building block affords a multi-stimuli-responsive dimer (FcD) with pre-determined double bond geometry, helical chirality, and relative orientation of the two ferrocene motifs in high yield. This intrinsically planar chiral switch can not only undergo thermal or photochemical E/Z isomerization but can also be reversibly and quantitatively oxidized to both a monocationic and a dicationic state which is associated with significant changes in its (chir)optical properties. Specifically, FcD acts as a chiral dopant for cholesteric LCs with a helical twisting power (HTP) of 13 µm-1 which, upon oxidation, drops to near zero, resulting in an unprecedently large redox-tuning of the LC reflection color by up to 84 nm. Due to the straightforward stereoselective synthesis, FcD, and related chiral switches, are envisioned to be powerful building blocks for multi-stimuli-responsive molecular machines and in LC-based materials.

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.

Klebsiella pneumoniae (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO3-2)-resistance (ter) operon as strongly associated with infection. However, TeO3-2 is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between ter and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the ter locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the ter operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available ter operon-encoding Kp plasmids, indicating that the ter operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the ter operon is dispensable during bacteremia, 2) the ter operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for ter. Furthermore, using 16S rRNA gene sequencing, we show that the ter operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a ter mutant. These findings indicate that the ter operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings.

Redox-Switchable Chalcogen Bonding for Anion Recognition and Sensing.

Inspired by the success of its related sigma-hole congener halogen bonding (XB), chalcogen bonding (ChB) is emerging as a powerful noncovalent interaction with a plethora of applications in supramolecular chemistry and beyond. Despite its increasing importance, the judicious modulation of ChB donor strength remains a formidable challenge. Herein, we present, for the first time, the reversible and large-scale modulation of ChB potency by electrochemical redox control. This is exemplified by both the switching-ON of anion recognition via ChB oxidative activation of a novel bis(ferrocenyltellurotriazole) anion host and switching-OFF reductive ChB deactivation of anion binding potency with a telluroviologen receptor. The direct linking of the redox-active center and ChB receptor donor sites enables strong coupling, which is reflected by up to a remarkable 3 orders of magnitude modulation of anion binding strength. This is demonstrated through large voltammetric perturbations of the respective receptor ferrocene and viologen redox couples, enabling, for the first time, ChB-mediated electrochemical anion sensing. The sensors not only display significant anion-binding-induced electrochemical responses in competitive aqueous-organic solvent systems but can compete with, or even outperform similar, highly potent XB and HB sensors. These observations serve to highlight a unique (redox) tunability of ChB and pave the way for further exploration of the reversible (redox) modulation of ChB in a wide range of applications, including anion sensors as well as molecular switches and machines.

Electrochemical Anion Sensing: Supramolecular Approaches.

Anions play a vital role in a broad range of environmental, technological, and physiological processes, making their detection/quantification valuable. Electroanalytical sensors offer much to the selective, sensitive, cheap, portable, and real-time analysis of anion presence where suitable combinations of selective (noncovalent) recognition and transduction can be integrated. Spurred on by significant developments in anion supramolecular chemistry, electrochemical anion sensing has received considerable attention in the past two decades. In this review, we provide a detailed overview of all electroanalytical techniques that have been used for this purpose, including voltammetric, impedimetric, capacititive, and potentiometric methods. We will confine our discussion to sensors that are based on synthetic anion receptors with a specific focus on reversible, noncovalent interactions, in particular, hydrogen- and halogen-bonding. Apart from their sensory properties, we will also discuss how electrochemical techniques can be used to study anion recognition processes (e.g., binding constant determination) and will furthermore provide a detailed outlook over future efforts and promising new avenues in this field.

Antifouling Strategies for Selective In Vitro and In Vivo Sensing.

The ability to fabricate sensory systems capable of highly selective operation in complex fluid will undoubtedly underpin key future developments in healthcare. However, the abundance of (bio)molecules in these samples can significantly impede performance at the transducing interface where nonspecific adsorption (fouling) can both block specific signal (reducing sensitivity) and greatly reduce assay specificity. Herein, we aim to provide a comprehensive review discussing concepts and recent advances in the construction of antifouling sensors that are, through the use of chemical, physical, or biological engineering, capable of operating in complex sample matrix (e.g., serum). We specifically highlight a range of molecular approaches to the construction of solid sensory interfaces (planar and nanoparticulate) and their characterization and performance in diverse in vitro and in vivo analyte (e.g., proteins, nucleic acids, cells, neuronal transmitters) detection applications via derived selective optical or electrochemical strategies. We specifically highlight those sensors that are capable of detection in complex media or those based on novel architectures/approaches. Finally, we provide perspectives on future developments in this rapidly evolving field.

Continuous and Polarization-Tuned Redox Capacitive Anion Sensing at Electroactive Interfaces.

Continuous, real-time ion sensing is of great value across various environmental and medical scenarios but remains underdeveloped. Herein, we demonstrate the potential of redox capacitance spectroscopy as a sensitive and highly adaptable ion sensing methodology, exemplified by the continuous flow sensing of anions at redox-active halogen bonding ferrocenylisophthalamide self-assembled monolayers. Upon anion binding, the redox distribution of the electroactive interface, and its associated redox capacitance, are reversibly modulated, providing a simple and direct sensory readout. Importantly, the redox capacitance can be monitored at a freely chosen, constant electrode polarization, providing a facile means of tuning both the sensor analytical performance and the anion binding affinity, by up to 1 order of magnitude. In surpassing standard voltammetric methods in terms of analytical performance and adaptability, these findings pave the way for the development of highly sensitive and uniquely tunable ion sensors. More generally, this methodology also serves as a powerful and unprecedented means of simultaneously modulating and monitoring the thermodynamics and kinetics of host-guest interactions at redox-active interfaces.

Solvent Effects in Halogen and Hydrogen Bonding Mediated Electrochemical Anion Sensing in Aqueous Solution and at Interfaces.

Sensing anionic species in competitive aqueous media is a well-recognised challenge to long-term applications across a multitude of fields. Herein, we report a comprehensive investigation of the electrochemical anion sensing performance of novel halogen bonding (XB) and hydrogen bonding (HB) bis-ferrocene-(iodo)triazole receptors in solution and at self-assembled monolayers (SAMs), in a range of increasingly competitive aqueous organic solvent media (ACN/H2 O). In solution, the XB sensor notably outperforms the HB sensor, with substantial anion recognition induced cathodic voltammetric responses of the ferrocene/ferrocenium redox couple persisting even in highly competitive aqueous solvent media of 20 % water content. The response to halides, in particular, shows a markedly lower sensitivity to increasing water content associated with a unique halide selectivity at unprecedented levels of solvent polarity. The HB sensor, in contrast, generally displayed a preference towards oxoanions. A significant surface-enhancement effect was observed for both XB/HB receptive films in all solvent systems, whereby the HB sensor generally displayed larger responses towards oxoanions than its halogen bonding analogue.

Halogen-Bonding Strapped Porphyrin BODIPY Rotaxanes for Dual Optical and Electrochemical Anion Sensing.

Anion receptors employing two distinct sensory mechanisms are rare. Herein, we report the first examples of halogen-bonding porphyrin BODIPY [2]rotaxanes capable of both fluorescent and redox electrochemical sensing of anions. 1 H NMR, UV/visible and electrochemical studies revealed rotaxane axle triazole group coordination to the zinc(II) metalloporphyrin-containing macrocycle component, serves to preorganise the rotaxane binding cavity and dramatically enhances anion binding affinities. Mechanically bonded, integrated-axle BODIPY and macrocycle strapped metalloporphyrin motifs enable the anion recognition event to be sensed by the significant quenching of the BODIPY fluorophore and cathodic perturbations of the metalloporphyrin P/P+. redox couple.

Real-time Voltammetric Anion Sensing Under Flow.

The development of real-life applicable ion sensors, in particular those capable of repeat use and long-term monitoring, remains a formidable challenge. Herein, we demonstrate, in a proof-of-concept, the real-time voltammetric sensing of anions under continuous flow in a 3D-printed microfluidic system. Electro-active anion receptive halogen bonding (XB) and hydrogen bonding (HB) ferrocene-isophthalamide-(iodo)triazole films were employed as exemplary sensory interfaces. Upon exposure to anions, the cathodic perturbations of the ferrocene redox-transducer are monitored by repeat square-wave voltammetry (SWV) cycling and peak fitting of the voltammograms by a custom-written MATLAB script. This enables the facile and automated data processing of thousands of SW scans and is associated with an over one order-of-magnitude improvement in limits of detection. In addition, this improved analysis enables tuning of the measurement parameters such that high temporal resolution can be achieved. More generally, this new flow methodology is extendable to a variety of other analytes, including cations, and presents an important step towards translation of voltammetric ion sensors from laboratory to real-world applications.

Reagentless Redox Capacitive Assaying of C-Reactive Protein at a Polyaniline Interface.

Methods that enable the sensitive and label-free detection of protein biomarkers are well-positioned to make potentially significant contributions to diagnostics and derived personalized healthcare. In support of this goal, a myriad of (electrochemical) methodologies have been developed; recently, electrochemical capacitance spectroscopy emerged as an impedance-derived approach which, in employing surface-confined redox-transducers, circumvents problems associated with the use of solution-phase redox-probes. Herein, we expand this scope by utilizing phytic acid-doped polyaniline as a novel redox-charging polymer support enabling the reagentless assaying of C-reactive protein in serum with good sensitivity. The construction of the sensory interface via electropolymerization allows facile tuning of the surface coverage and redox (capacitive) properties of the polymers, which, in turn, modulate both assay selectivity, fouling, and sensitivity. Significantly, this methodology is readily extendable to a wide range of electrode materials and analytes.

Serum neuronal exosomes predict and differentiate Parkinson's disease from atypical parkinsonism.

OBJECTIVE: Parkinson's disease is characterised neuropathologically by α-synuclein aggregation. Currently, there is no blood test to predict the underlying pathology or distinguish Parkinson's from atypical parkinsonian syndromes. We assessed the clinical utility of serum neuronal exosomes as biomarkers across the spectrum of Parkinson's disease, multiple system atrophy and other proteinopathies. METHODS: We performed a cross-sectional study of 664 serum samples from the Oxford, Kiel and Brescia cohorts consisting of individuals with rapid eye movement sleep behavioural disorder, Parkinson's disease, dementia with Lewy bodies, multiple system atrophy, frontotemporal dementia, progressive supranuclear palsy, corticobasal syndrome and controls. Longitudinal samples were analysed from Parkinson's and control individuals. We developed poly(carboxybetaine-methacrylate) coated beads to isolate L1 cell adhesion molecule (L1CAM)-positive extracellular vesicles with characteristics of exosomes and used mass spectrometry or multiplexed electrochemiluminescence to measure exosomal proteins. RESULTS: Mean neuron-derived exosomal α-synuclein was increased by twofold in prodromal and clinical Parkinson's disease when compared with multiple system atrophy, controls or other neurodegenerative diseases. With 314 subjects in the training group and 105 in the validation group, exosomal α-synuclein exhibited a consistent performance (AUC=0.86) in separating clinical Parkinson's disease from controls across populations. Exosomal clusterin was elevated in subjects with non-α-synuclein proteinopathies. Combined neuron-derived exosomal α-synuclein and clusterin measurement predicted Parkinson's disease from other proteinopathies with AUC=0.98 and from multiple system atrophy with AUC=0.94. Longitudinal sample analysis showed that exosomal α-synuclein remains stably elevated with Parkinson's disease progression. CONCLUSIONS: Increased α-synuclein egress in serum neuronal exosomes precedes the diagnosis of Parkinson's disease, persists with disease progression and in combination with clusterin predicts and differentiates Parkinson's disease from atypical parkinsonism.

The nanoscopic principles of capacitive ion sensing interfaces.

Herein we discuss the operational principles of molecular interfaces that specifically recruit ions from an electrolyte solution and report this in a reagentless capacitive manner. At low ionic occupancy the response of the interface obeys a Debye-type phenomenon akin to classic "image charge" effects. At higher levels of occupancy, the response follows Thomas-Fermi screening and, significantly, is dependent on the electronic structure of the mesoscopic ion-receptor host-guest ensemble.

Redox Capacitive Assaying of C-Reactive Protein at a Peptide Supported Aptamer Interface.

Electrochemical immunosensors offer much in the potential translation of a lab based sensing capability to a useful "real world" platform. In previous work we have introduced an impedance-derived electrochemical capacitance spectroscopic analysis as supportive of a reagentless means of reporting on analyte target capture at suitably prepared mixed-component redox-active, antibody-modified interfaces. Herein we directly integrate receptive aptamers into a redox charging peptide support in enabling a label-free low picomolar analytical assay for C-reactive protein with a sensitivity that significantly exceeds that attainable with an analogous antibody interface.

Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril.

We introduce herein boron-dipyrromethene (BODIPY) dyes as a new class of fluorophores for the design of reporter dyes for supramolecular host-guest complex formation with cucurbit[7]uril (CB7). The BODIPYs contain a protonatable aniline nitrogen in the meso-position of the BODIPY chromophore, which was functionalized with known binding motifs for CB7. The unprotonated dyes show low fluorescence due to photoinduced electron transfer (PET), whereas the protonated dyes are highly fluorescent. Encapsulation of the binding motif inside CB7 positions the aniline nitrogen at the carbonyl rim of CB7, which affects the pKa value, and leads to a host-induced protonation and thus to a fluorescence increase. The possibility to tune binding affinities and pKa values is demonstrated and it is shown that, in combination with the beneficial photophysical properties of BODIPYs, several new applications of host-dye reporter pairs can be implemented. This includes indicator displacement assays with favourable absorption and emission wavelengths in the visible spectral region, fluorescence correlation spectroscopy, and noncovalent surface functionalization with fluorophores.

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.

Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.