Elucidating the binding properties of methemoglobin in red blood cell to cyanide, hydrosulfide, and azide ions using artificial red blood cell.

Methemoglobin (metHb), the oxidized form of hemoglobin, lacks the ability of reversible oxygen binding; however, it has a high binding affinity to toxic substances such as cyanide, hydrosulfide, and azide. This innate property of metHb offers the clinical option to treat patients poisoned with these toxins, by oxidizing the endogenous hemoglobin in the red blood cells (RBCs). The binding properties of naked metHb (isolated from RBC) with these toxins has been studied; however, the binding behaviors of metHb under the intracellular conditions of RBC are unclear because of the difficulty in detecting metHb status changes in RBC. This study aimed to elucidate the binding properties of metHb in RBC under physiological and poisoned conditions using artificial RBC, which was hemoglobin encapsulated in a liposome. The mimic-circumstances of metHb in RBC (metHb-V) was prepared by oxidizing the hemoglobin in artificial RBC. Spectroscopic analysis indicated that the metHb in metHb-V exhibited a binding behavior different from that of naked metHb, depending on the toxic substance: When the pH decreased, (i) the cyanide binding affinity of metHb-V remained unchanged, but that of naked metHb decreased (ii) the hydrosulfide binding affinity was increased in metHb-V but was decreased in naked metHb. (iii) Azide binding was increased in metHb-V, which was similar to that in naked metHb, irrespective of the pH change. Thus, the binding behavior of intracellular metHb in the RBC with cyanide, hydrosulfide, and azide under physiological and pathological conditions were partly elucidated using the oxidized artificial RBC.

Profiling sirtuin activity using Copper-free click chemistry.

The mammalian sirtuins are a group of posttranslational modification enzymes that remove acyl modifications from lysine residues in an NAD+-dependent manner. Although initially proposed as histone deacetylases (HDACs), they are now known to target other cellular enzymes and proteins as well. Sirtuin-catalyzed simple amide hydrolysis has profound biological consequences including suppression of gene expression, promotion of DNA damage repair, and regulation of glucose and lipid metabolism. Human sirtuins have been intensively pursued by both academia and industry as potential therapeutic targets for the treatment of diseases such as cancer and neurodegeneration. To gain a better understanding of their roles in various cellular events, innovative chemical probes are highly sought after. This current study focuses on the development of activity-based chemical probes (ABPs) for the profiling of sirtuin activity in biological samples. Cyclooctyne-containing and azido-containing probes were synthesized to enable the subsequent copper-free "click" conjugation to either a fluorophore or biotin. The two groups of structurally related ABPs demonstrated different labeling efficiency and selectivity: the cyclooctyne-containing probes failed to label recombinant sirtuins to any appreciable level, while the azido-containing ABPs showed good isoform selectivity. The azido-containing ABPs were further analyzed for their ability to label an individual sirtuin isoform in protein mixtures and cell lysates. These biocompatible ABPs allow the study of dynamic cellular protein activity change to become possible.

Changes in physico-chemical characteristics and viable bacterial communities during fermentation of alfalfa silages inoculated with Lactobacillus plantarum.

This study investigated the effect of inoculating Lactobacillus (L.) plantarum PS-8 in fermentation of alfalfa silages. We monitored the fermentation characteristics and bacterial population dynamics during the ensiling process. PacBio single molecule real time sequencing was combined with propidium monoazide (PMA) treatment to monitor the viable microbiota dynamics. We found that inoculating L. plantarum PS-8 may improve the silage quality by accelerating acidification, reducing the amounts of clostridia, coliform bacteria, molds and yeasts, elevating the protein and organic acid contents (except butyrate), and enhancing lactic acid bacteria (LAB) while suppressing harmful microorganisms. Some significant differential abundant taxa were found between the PMA-treated and non-treated microbiota. For example, the relative abundances of L. brevis, L. plantarum, and Pediococcus pentosaceus were significantly higher in the PMA-treated group than the non-PMA-treated group, suggesting obvious differences between the viable and non-viable microbiota. It would thus be necessary to distinguish between the viable and non-viable microbial communities to further understand their physiological contribution in silage fermentation. By tracking the dynamics of viable microbiota in relation with changes in the physico-chemical parameters, our study provided novel insights into the beneficial effects of inoculating L. plantarum PS-8 in silage fermentation and the physiological function of the viable bacterial communities.

Evaluation of dual electrode configurations for microchip electrophoresis used for voltammetric characterization of electroactive species.

Microchip electrophoresis coupled with amperometric detection is more popular than voltammetric detection due to the lower limits of detection that can be achieved. However, voltammetry provides additional information about the redox properties of the analyte that can be used for peak identification. In this paper, two dual electrode configurations for microchip electrophoresis are described and evaluated for obtaining voltammetric information using amperometry. The dual-series electrode configuration was first evaluated to generate current ratios in a single run by applying two different potentials to the working electrodes placed perpendicular to the separation channel. However, it was found that it is difficult to obtain realistic current ratios with this configuration, primarily due to the relative placement of electrodes with respect to the channel end of the simple-t microchip. Correction factors were needed to obtain current ratios similar to those that would be obtained for sequential injections at two different potentials using a single electrode. A second approach using a dual-channel chip with two parallel electrodes was then developed and evaluated for obtaining voltammetric identification. The newly developed microchip permitted the injection of same amount of sample into two unique separation channels, each with an electrode at a different detection potential. Migration times and current ratios for several biologically important molecules and potential interferences including nitrite, tyrosine, hydrogen peroxide, and azide were obtained and compared to the responses obtained for analytes found in macrophage cell lysates.

New perspectives on aryl azide noncanonical amino acid use in yeast.

A photochemically chemically active noncanonical amino acid para-azido-l-phenylalanine widely used in biology was found to be metabolized by Saccharomyces cerevisiae. Contrary to multiple reports, the azide moiety is not reduced to the corresponding amine. The amino acid's concentration was found to decline somewhat with time which was due, at least in part, to modification of the amino acid side chain. The metabolite was found to be photochemically active and further characterization concluded the azide moiety was still intact. This work also goes onto highlight paramount areas of concern with regards to (photo)chemical compatibility, handling, and fidelity in genetically encoding aryl azide amino acids.

Screen-printed Microsensors Using Polyoctyl-thiophene (POT) Conducting Polymer As Solid Transducer for Ultratrace Determination of Azides.

Two novel all-solid-state potentiometric sensors for the determination of azide ion are prepared and described here for the first time. The sensors are based on the use of iron II-phthalocyanine (Fe-PC) neutral carrier complex and nitron-azide ion-pair complex (Nit-N3-) as active recognition selective receptors, tetradodecylammonium tetrakis(4-chlorophenyl) borate (ETH 500) as lipophilic cationic additives and poly(octylthiophene) (POT) as the solid contact material on carbon screen-printed devices made from a ceramic substrate. The solid-contact material (POT) is placed on a carbon substrate (2 mm diameter) by drop-casting, followed, after drying, by coating with a plasticized PVC membrane containing the recognition sensing complexes. Over the pH range 6-9, the sensors display fast (< 10 s), linear potentiometric response for 1.0 × 10-2⁻1.0 × 10-7 M azide with low detection limit of 1.0 × 10-7 and 7.7 × 10-8 M (i.e., 6.2⁻4.8 ng/ml) for Fe-PC/POT/and Nit-N3-/POT based sensors, respectively. The high potential stability and sensitivity of the proposed sensors are confirmed by electrochemical impedance spectroscopy (EIS) and constant-current chronopotentiometry measurement techniques. Strong membrane adhesion and absence of delamination of the membrane, due to possible formation of a water film between the recognition membranes and the electron conductor are also verified. The proposed sensors are successfully applied for azide quantification in synthetic primer mixture samples. Advantages offered by these sensors are the robustness, ease of fabrication, simple operation, stable potential response, high selectivity, good sensitivity and low cost.

Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray.

O-GalNAc glycosylation is the initial step of the mucin-type O-glycosylation. In humans, it is catalyzed by a family of 20 homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). So far, there is very limited information on their protein substrate specificities. In this study, we developed an on-chip ppGalNAc-Ts assay that could rapidly and systematically identify the protein substrates of each ppGalNAc-T. In detail, we utilized a human proteome microarray as the protein substrates and UDP-GalNAz as the nucleotide sugar donor for click chemistry detection. From a total of 16 368 human proteins, we identified 570 potential substrates of ppGalNAc-T1, T2, and T3. Among them, 128 substrates were overlapped, while the rest were isoform specific. Further cluster analysis of these substrates showed that the substrates of ppGalNAc-T1 had a closer phylogenetic relationship with that of ppGalNAc-T3 compared with ppGalNAc-T2, which was consistent with the topology of the phylogenetic tree of these ppGalNAc-Ts. Taken together, our microarray-based enzymatic assay comprehensively reveals the substrate profile of the ppGalNAc-T1, T2, and T3, which not only provides a plausible explanation for their partial functional redundancy as reported, but clearly implies some specialized roles of each enzyme in different biological processes.

Selective Imaging of Gram-Negative and Gram-Positive Microbiotas in the Mouse Gut.

The diverse gut microbial communities are crucial for host health. How the interactions between microbial communities and between host and microbes influence the host, however, is not well understood. To facilitate gut microbiota research, selective imaging of specific groups of microbiotas in the gut is of great utility but remains technically challenging. Here we present a chemical approach that enables selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut by exploiting their distinctive cell wall components. Cell-selective labeling is achieved by the combined use of metabolic labeling of Gram-negative bacterial lipopolysaccharides with a clickable azidosugar and direct labeling of Gram-positive bacteria with a vancomycin-derivatized fluorescent probe. We demonstrated this strategy by two-color fluorescence imaging of Gram-negative and Gram-positive gut microbiotas in the mouse intestines. This chemical method should be broadly applicable to different gut microbiota research fields and other bacterial communities studied in microbiology.

Assessing the Delivery of Molecules to the Mitochondrial Matrix Using Click Chemistry.

Mitochondria are central to health and disease, hence there is considerable interest in developing mitochondria-targeted therapies that require the delivery of peptides or nucleic acid oligomers. However, progress has been impeded by the lack of a measure of mitochondrial import of these molecules. Here, we address this need by quantitatively detecting molecules within the mitochondrial matrix. We used a mitochondria- targeted cyclooctyne (MitoOct) that accumulates several- hundredfold in the matrix, driven by the membrane potential. There, MitoOct reacts through click chemistry with an azide on the target molecule to form a diagnostic product that can be quantified by mass spectrometry. Because the membrane potential-dependent MitoOct concentration in the matrix is essential for conjugation, we can now determine definitively whether a putative mitochondrion-targeted molecule reaches the matrix. This "ClickIn" approach will facilitate development of mitochondria-targeted therapies.

Tracking G-protein-coupled receptor activation using genetically encoded infrared probes.

Rhodopsin is a prototypical heptahelical family A G-protein-coupled receptor (GPCR) responsible for dim-light vision. Light isomerizes rhodopsin's retinal chromophore and triggers concerted movements of transmembrane helices, including an outward tilting of helix 6 (H6) and a smaller movement of H5, to create a site for G-protein binding and activation. However, the precise temporal sequence and mechanism underlying these helix rearrangements is unclear. We used site-directed non-natural amino acid mutagenesis to engineer rhodopsin with p-azido-l-phenylalanine residues incorporated at selected sites, and monitored the azido vibrational signatures using infrared spectroscopy as rhodopsin proceeded along its activation pathway. Here we report significant changes in electrostatic environments of the azido probes even in the inactive photoproduct Meta I, well before the active receptor state was formed. These early changes suggest a significant rotation of H6 and movement of the cytoplasmic part of H5 away from H3. Subsequently, a large outward tilt of H6 leads to opening of the cytoplasmic surface to form the active receptor photoproduct Meta II. Thus, our results reveal early conformational changes that precede larger rigid-body helix movements, and provide a basis to interpret recent GPCR crystal structures and to understand conformational sub-states observed during the activation of other GPCRs.

Targeted Ultrasound-Assisted Cancer-Selective Chemical Labeling and Subsequent Cancer Imaging using Click Chemistry.

Metabolic sugar labeling followed by the use of reagent-free click chemistry is an established technique for in vitro cell targeting. However, selective metabolic labeling of the target tissues in vivo remains a challenge to overcome, which has prohibited the use of this technique for targeted in vivo applications. Herein, we report the use of targeted ultrasound pulses to induce the release of tetraacetyl N-azidoacetylmannosamine (Ac4 ManAz) from microbubbles (MBs) and its metabolic expression in the cancer area. Ac4 ManAz-loaded MBs showed great stability under physiological conditions, but rapidly collapsed in the presence of tumor-localized ultrasound pulses. The released Ac4 ManAz from MBs was able to label 4T1 tumor cells with azido groups and significantly improved the tumor accumulation of dibenzocyclooctyne (DBCO)-Cy5 by subsequent click chemistry. We demonstrated for the first time that Ac4 ManAz-loaded MBs coupled with the use of targeted ultrasound could be a simple but powerful tool for in vivo cancer-selective labeling and targeted cancer therapies.

Line shape analysis of two-dimensional infrared spectra.

Ultrafast two-dimensional infrared (2D IR) spectroscopy probes femtosecond to picosecond time scale dynamics ranging from solvation to protein motions. The frequency-frequency correlation function (FFCF) is the quantitative measure of the spectral diffusion that reports those dynamics and, within certain approximations, can be extracted directly from 2D IR line shapes. A variety of methods have been developed to extract the FFCF from 2D IR spectra, which, in principle, should give the same FFCF parameters, but the complexity of real experimental systems will affect the results of these analyses differently. Here, we compare five common analysis methods using both simulated and experimental 2D IR spectra to understand the effects of apodization, anharmonicity, phasing errors, and finite signal-to-noise ratios on the results of each of these analyses. Our results show that although all of the methods can, in principle, yield the FFCF under idealized circumstances, under more realistic experimental conditions they behave quite differently, and we find that the centerline slope analysis yields the best compromise between the effects we test and is most robust to the distortions that they cause.

Highly sensitive fluorescence and SERS detection of azide through a simple click reaction of 8-chloroquinoline and phenylacetylene.

In 0.19 mol/L acetic acid (HAc), a click reaction of 8-chloroquinoline/azide/phenylacetylene take places in aqueous solution without Cu(I) as a catalyst. 8-Chloroquinoline (CQN) exhibited a strong fluorescence peak at 430 nm that was quenched linearly as the concentration of azide increased from 20 to 1000 ng/mL. This quenching was due to consumption of CQN in the click reaction and a decrease in the number of efficiently excited photons due to the presence of triazole-quinoline ramification molecules with strong hydrophobicity. Using blue nanosilver sol as the substrate, CQN absorbed onto the surface of nanosilver particles, showing a strong surface-enhanced Raman scattering (SERS) peak at 1585 cm(-1) that decreased linearly as the azide concentration increased from 8 to 500 ng/mL; the detection limit was 4 ng/mL. Thus, two new, simple and sensitive fluorescence and SERS methods have been developed for the determination of azide via the click reaction.

Multiple poisonings with sodium azide at a local restaurant.

BACKGROUND: Sodium azide is a chemical with a mechanism similar to cyanide. There is concern that it could be used as a chemical warfare agent. OBJECTIVES: We report a cluster of poisonings that occurred at a public restaurant and the subsequent investigation that identified iced tea contaminated with sodium azide (NaN3) and hydrazoic acid, as the foodborne vehicle and agents, respectively. CASE REPORT: Five patients became ill within minutes of drinking iced tea at a restaurant. They all presented to the same Emergency Department with similar symptoms, and improved with fluids, antiemetics, and supportive care. A joint investigation by the Dallas County Department of Health and Human Services, the Texas State Health Department, the Dallas County Southwestern Institute of Forensic Sciences, and the medical toxicologists at the University of Texas Southwestern School of Medicine identified iced tea, contaminated with sodium azide (NaN3) and hydrazoic acid, as the foodborne vehicle and agents, respectively. CONCLUSION: The recurrence, and seriousness, of these events suggests a need for continued education of emergency providers. Emergency physicians should consider exposures to toxic chemicals in their differential when a cluster of patients presents with similar symptoms over a short period of time.

Optimization, validation, and application of a real-time PCR protocol for quantification of viable bacterial cells in municipal sewage sludge and biosolids using reporter genes and Escherichia coli.

Biosolids result from treatment of sewage sludge to meet jurisdictional standards, including pathogen reduction. Once government regulations are met, materials can be applied to agricultural lands. Culture-based methods are used to enumerate pathogen indicator microorganisms but may underestimate cell densities, which is partly due to bacteria existing in a viable but non-culturable physiological state. Viable indicators can also be quantified by realtime polymerase chain reaction (qPCR) used with propidium monoazide (PMA), a dye that inhibits amplification of DNA found extracellularly or in dead cells. The objectives of this study were to test an optimized PMA-qPCR method for viable pathogen detection in wastewater solids and to validate it by comparing results to data obtained by conventional plating. Reporter genes from genetically marked Pseudomonas sp. UG14Lr and Agrobacterium tumefaciens 542 cells were spiked into samples of primary sludge, and anaerobically digested and Lystek-treated biosolids as cell-free DNA, dead cells, viable cells, and mixtures of live and dead cells, followed by DNA extraction with and without PMA, and qPCR. The protocol was then used for Escherichia coli quantification in the three matrices, and results compared to plate counts. PMA-qPCR selectively detected viable cells, while inhibiting signals from cell-free DNA and DNA found in membrane-compromised cells. PMA-qPCR detected 0.5-1 log unit more viable E. coli cells in both primary solids and dewatered biosolids than plate counts. No viable E. coli was found in Lystek-treated biosolids. These data suggest PMA-qPCR may more accurately estimate pathogen cell numbers than traditional culture methods.

Cell-selective metabolic glycan labeling based on ligand-targeted liposomes.

A cell-specific metabolic glycan labeling strategy has been developed using azidosugars encapsulated in ligand-targeted liposomes. The ligands are designed to bind specific cell-surface receptors that are only expressed or up-regulated in target cells, which mediates the intracellular delivery of azidosugars. The delivered azidosugars are metabolically incorporated into cell-surface glycans, which are then imaged via a bioorthogonal reaction.

Metabolic oligosaccharide engineering with N-Acyl functionalized ManNAc analogs: cytotoxicity, metabolic flux, and glycan-display considerations.

Metabolic oligosaccharide engineering (MOE) is a maturing technology capable of modifying cell surface sugars in living cells and animals through the biosynthetic installation of non-natural monosaccharides into the glycocalyx. A particularly robust area of investigation involves the incorporation of azide functional groups onto the cell surface, which can then be further derivatized using "click chemistry." While considerable effort has gone into optimizing the reagents used for the azide ligation reactions, less optimization of the monosaccharide analogs used in the preceding metabolic incorporation steps has been done. This study fills this void by reporting novel butanoylated ManNAc analogs that are used by cells with greater efficiency and less cytotoxicity than the current "gold standard," which are peracetylated compounds such as Ac4 ManNAz. In particular, tributanoylated, N-acetyl, N-azido, and N-levulinoyl ManNAc analogs with the high flux 1,3,4-O-hydroxyl pattern of butanoylation were compared with their counterparts having the pro-apoptotic 3,4,6-O-butanoylation pattern. The results reveal that the ketone-bearing N-levulinoyl analog 3,4,6-O-Bu3 ManNLev is highly apoptotic, and thus is a promising anti-cancer drug candidate. By contrast, the azide-bearing analog 1,3,4-O-Bu3 ManNAz effectively labeled cellular sialoglycans at concentrations ∼3- to 5-fold lower (e.g., at 12.5-25 µM) than Ac4 ManNAz (50-150 µM) and exhibited no indications of apoptosis even at concentrations up to 400 µM. In summary, this work extends emerging structure activity relationships that predict the effects of short chain fatty acid modified monosaccharides on mammalian cells and also provides a tangible advance in efforts to make MOE a practical technology for the medical and biotechnology communities.

Highly selective organic fluorescent probe for azide ion: formation of a "molecular ring".

An indole based naphthalene derivative is reported as a highly selective fluorescent probe for azide ion in aqueous ethanol. The probe is applied for cell imaging of the N(3)(-) ion in contaminated living cells. Both experimental and theoretical studies have been performed to figure out the plausible mechanism of fluorescence enhancement of the probe upon binding with N(3)(-).

Determination of azide in gastric fluid and urine by flow-injection electrospray ionization tandem mass spectrometry.

A rapid method was developed to identify and quantify the azide ion (N(3)(-)) in gastric fluid and urine. N(3)(-) in diluted biological fluids was reacted with NaAuCl(4) to produce Au(N(3))(2)(-), which was extracted with octanol. Five microliters of the extract were flow-injected into an electrospray ionization tandem mass spectrometric instrument. Quantification of N(3)(-) was performed by selected reaction monitoring of the product ion Au(N)(N(3))(-) at m/z 253, which was derived from the precursor ion Au(N(3))(2)(-) at m/z 281, using 50 µL of aqueous solution within 10 min. This method was found to be linear up to 10(-5) M, to have a limit of quantification of 10(-7) M, a limit of detection of 3.0 × 10(-8) M, and a coefficient of variation of ≦10% at 10(-7) M. In the case of urine, 50 µL of urine were spiked with N(3)(-), this was diluted 10-fold and passed through 1 mL of a resin, and finally diluted to 100-fold of the original. This method was linear up to 10(-3) M, had a limit of quantification of 10(-5) M, a limit of detection of 3.0 × 10(-6) M, and coefficient of variation of ≦8.8% for an original urine concentration of 10(-5) M. The practical applicability of this method was checked by diluting 1 µL of a suspected suicide victim's gastric fluid 20,000-fold and 1 µL of the victim's urine 5,000-fold and then measuring the N(3)(-) levels. These levels were found to be (7.5 ± 1.0) × 10(-2) M and (3.2 ± 0.4) × 10(-3) M, respectively.

Synthesis and characterization of the phosphorus triazides OP(N3)3 and SP(N3)3.

Two explosive triazides of phosphorus(V), OP(N(3))(3) and SP(N(3))(3), have been prepared as neat substances and structurally characterized. Both compounds can be handled in gas, liquid, and solid states in submillimolar quantities. The melting points of OP(N(3))(3) and SP(N(3))(3) are +22 and -30 °C, respectively. The two triazides have been characterized by IR (Ar matrix and gas phase) and Raman (solid) spectroscopies. Their single-crystal structures were obtained by X-ray diffraction and found to be significantly distorted from the predicted ideal C(3) symmetry because of intermolecular interactions. The spectroscopic and structural properties are discussed in combination with density functional theory calculations.