Formaldehyde (FA) is a common environmental toxin that is also produced naturally in the body through a wide range of metabolic and epigenetic processes, motivating the development of new ...technologies to monitor this reactive carbonyl species (RCS) in living systems. Herein, we report a pair of first‐generation chemiluminescent probes for selective formaldehyde detection. Caging phenoxy‐dioxetane scaffolds bearing different electron‐withdrawing groups with a general 2‐aza‐Cope reactive formaldehyde trigger provides chemiluminescent formaldehyde probes 540 and 700 (CFAP540 and CFAP700) for visible and near‐IR detection of FA in living cells and mice, respectively. In particular, CFAP700 is capable of visualizing FA release derived from endogenous folate metabolism, providing a starting point for the use of CFAPs and related chemical tools to probe FA physiology and pathology, as well as for the development of a broader palette of chemiluminescent activity‐based sensing (ABS) probes that can be employed from in vitro biochemical to cell to animal models.
Metabolic sensing: A first‐generation set of chemiluminescent activity‐based probes for in vivo imaging of formaldehyde (FA) is reported. A FA‐selective trigger is used to cage a phenoxy‐dioxetane scaffold that emits a photon after aza‐Cope‐dependent uncaging. These reagents were used to image FA fluxes in living cells and mice, enabling the unique identification of endogenous FA production from metabolic folate cycles in vivo.
Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased ...environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms. We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls. Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases—the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure—as well as the high correlation (r ² = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes. Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.
Bioluminescence imaging is a powerful modality for in vivo imaging owing to its low background and high signal-to-noise ratio. Because bioluminescent emission occurs only upon the catalytic reaction ...between the luciferase enzyme and its luciferin substrate, caging luciferins with analyte-reactive triggers offers a general approach for activity-based sensing of specific biochemical processes in living systems across cell, tissue, and animal models. In this review, we summarize recent efforts in the development of synthetic caged luciferins for tracking enzyme, small molecule, and metal ion activity and their contributions to physiological and pathological processes.
A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of ...stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur-methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.
The recent discovery of mutations in metabolic enzymes has rekindled interest in harnessing the altered metabolism of cancer cells for cancer therapy. One potential drug target is isocitrate ...dehydrogenase 1 (IDH1), which is mutated in multiple human cancers. Here, we examine the role of mutant IDH1 in fully transformed cells with endogenous IDH1 mutations. A selective R132H-IDH1 inhibitor (AGI-5198) identified through a high-throughput screen blocked, in a dose-dependent manner, the ability of the mutant enzyme (m1DH1) to produce R-2-hydroxyglutarate (R-2HG). Under conditions of near-complete R-2HG inhibition, the m1DH1 inhibitor induced demethylation of histone H3K9me3 and expression of genes associated with gliogenic differentiation. Blockade of m1DH1 impaired the growth of IDH1-mutant—but not IDH1-wild-type—glioma cells without appreciable changes in genome-wide DNA methylation. These data suggest that m1DH1 may promote glioma growth through mechanisms beyond its well-characterized epigenetic effects.
The field of single-molecule electronics harnesses expertise from engineering, physics and chemistry to realize circuit elements at the limit of miniaturization; it is a subfield of nanoelectronics ...in which the electronic components are single molecules. In this Review, we survey the field from a chemical perspective and discuss the structure–property relationships of the three components that form a single-molecule junction: the anchor, the electrode and the molecular bridge. The spatial orientation and electronic coupling between each component profoundly affect the conductance properties and functions of the single-molecule device. We describe the design principles of the anchor group, the influence of the electronic configuration of the electrode and the effect of manipulating the structure of the molecular backbone and of its substituent groups. We discuss single-molecule conductance switches as well as the phenomenon of quantum interference and then trace their fundamental roots back to chemical principles.Single-molecule electronic junctions comprise three components: anchors, electrodes and the molecular bridge. This Review surveys the relationship between the chemical structures and the electronic properties of each component, and extends the discussion to switching functions and the phenomenon of quantum interference.
The tunnelling of electrons through molecules (and through any nanoscale insulating and dielectric material
) shows exponential attenuation with increasing length
, a length dependence that is ...reflected in the ability of the electrons to carry an electrical current. It was recently demonstrated
that coherent tunnelling through a molecular junction can also be suppressed by destructive quantum interference
, a mechanism that is not length-dependent. For the carbon-based molecules studied previously, cancelling all transmission channels would involve the suppression of contributions to the current from both the π-orbital and σ-orbital systems. Previous reports of destructive interference have demonstrated a decrease in transmission only through the π-channel. Here we report a saturated silicon-based molecule with a functionalized bicyclo2.2.2octasilane moiety that exhibits destructive quantum interference in its σ-system. Although molecular silicon typically forms conducting wires
, we use a combination of conductance measurements and ab initio calculations to show that destructive σ-interference, achieved here by locking the silicon-silicon bonds into eclipsed conformations within a bicyclic molecular framework, can yield extremely insulating molecules less than a nanometre in length. Our molecules also exhibit an unusually high thermopower (0.97 millivolts per kelvin), which is a further experimental signature of the suppression of all tunnelling paths by destructive interference: calculations indicate that the central bicyclo2.2.2octasilane unit is rendered less conductive than the empty space it occupies. The molecular design presented here provides a proof-of-concept for a quantum-interference-based approach to single-molecule insulators.
We show that the three conformational states of integrin α5β1 have discrete free energies and define activation by measuring intrinsic affinities for ligand of each state and the equilibria linking ...them. The 5,000‐fold higher affinity of the extended‐open state than the bent‐closed and extended‐closed states demonstrates profound regulation of affinity. Free energy requirements for activation are defined with protein fragments and intact α5β1. On the surface of K562 cells, α5β1 is 99.8% bent‐closed. Stabilization of the bent conformation by integrin transmembrane and cytoplasmic domains must be overcome by cellular energy input to stabilize extension. Following extension, headpiece opening is energetically favored. N‐glycans and leg domains in each subunit that connect the ligand‐binding head to the membrane repel or crowd one another and regulate conformational equilibria in favor of headpiece opening. The results suggest new principles for regulating signaling in the large class of receptors built from extracellular domains in tandem with single‐span transmembrane domains.
Synopsis
Thermodynamic analysis of the three integrin α5β1 conformation states offers a model for signaling regulation via an interplay between extracellular and transmembrane/intracellular domains in a large class of receptors built from multiple domains.
The integrin extended‐open state has 5,000‐fold higher ligand affinity than the bent‐closed and extended‐closed states.
Interactions between N‐glycosylated leg domains of integrin alpha and beta subunits regulate conformational equilibria in favor of headpiece opening.
Almost all α5β1 integrins on the cell surface are in a bent‐closed conformation.
Stabilization of the bent conformation by integrin transmembrane and cytoplasmic domains must be overcome by cellular energy input to establish the high affinity, extended‐open state.
Thermodynamic and intrinsic affinity measurements show how intramolecular interactions of integrin receptor domains and post‐translational modifications regulate activation of ligand binding.
The retina is a widely profiled tissue in multiple species by single-cell RNA sequencing studies. However, integrative research of the retina across species is lacking. Here, we construct the first ...single-cell atlas of the human and porcine ocular compartments and study inter-species differences in the retina. In addition to that, we identify putative adult stem cells present in the iris tissue. We also create a disease map of genes involved in eye disorders across compartments of the eye. Furthermore, we probe the regulons of different cell populations, which include transcription factors and receptor-ligand interactions and reveal unique directional signalling between ocular cell types. In addition, we study conservation of regulons across vertebrates and zebrafish to identify common core factors. Here, we show perturbation of KLF7 gene expression during retinal ganglion cells differentiation and conclude that it plays a significant role in the maturation of retinal ganglion cells.
Tests that predict outcomes for patients with acute myeloid leukemia (AML) are imprecise, especially for those with intermediate risk AML.
To determine whether genomic approaches can provide novel ...prognostic information for adult patients with de novo AML.
Whole-genome or exome sequencing was performed on samples obtained at disease presentation from 71 patients with AML (mean age, 50.8 years) treated with standard induction chemotherapy at a single site starting in March 2002, with follow-up through January 2015. In addition, deep digital sequencing was performed on paired diagnosis and remission samples from 50 patients (including 32 with intermediate-risk AML), approximately 30 days after successful induction therapy. Twenty-five of the 50 were from the cohort of 71 patients, and 25 were new, additional cases.
Whole-genome or exome sequencing and targeted deep sequencing. Risk of identification based on genetic data.
Mutation patterns (including clearance of leukemia-associated variants after chemotherapy) and their association with event-free survival and overall survival.
Analysis of comprehensive genomic data from the 71 patients did not improve outcome assessment over current standard-of-care metrics. In an analysis of 50 patients with both presentation and documented remission samples, 24 (48%) had persistent leukemia-associated mutations in at least 5% of bone marrow cells at remission. The 24 with persistent mutations had significantly reduced event-free and overall survival vs the 26 who cleared all mutations. Patients with intermediate cytogenetic risk profiles had similar findings. table: see text.
The detection of persistent leukemia-associated mutations in at least 5% of bone marrow cells in day 30 remission samples was associated with a significantly increased risk of relapse, and reduced overall survival. These data suggest that this genomic approach may improve risk stratification for patients with AML.
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