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.

Toxicological analysis of azide and cyanide for azide intoxications using gas chromatography.

Azide is a highly toxic chemical agent to human being. Accidental, but also intentional exposure to azide occurs. To be able to confirm azide ingestion, we developed a method to identify and quantify azide in biological matrices. Cyanide was included in the method to evaluate suggested in vivo production of cyanide after azide ingestion. Azide in biological matrices was first derivatized by propionic anhydride to form propionyl azide. Simultaneously, cyanide was converted into hydrogen cyanide. After thermal rearrangement of propionyl azide, ethyl isocyanate was formed, separated together with hydrogen cyanide by gas chromatography (GC) and detected using a nitrogen phosphorous detector (NPD). The method was linear from 1.0-100 µg/mL for both analytes, and azide was stable in human plasma at -20°C for at least 49 days. Azide was measured in the gastric content of two cases of suspected azide ingestion (case 1:1.2 mg/mL, case 2:1.5 mg/mL). Cyanide was only identified in the gastric content of case 1 (approximately 1.4 µg/mL). Furthermore, azide was quantified in plasma (19 µg/mL), serum (24 µg/mL), cell pellet (21 µg/mL) and urine (3.0 µg/mL) of case 2. This method can be used to confirm azide and cyanide exposure, and azide concentrations can be quantified in several biological matrices.

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.

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.

A Unified Framework for the Incorporation of Bioorthogonal Compound Exposure Probes within Biological Compartments.

Compartmentalization is a crucial facet of many biological systems, and key aspects of cellular processes rely on spatial segregation within the cell. While many drug targets reside in specific intracellular compartments, the tools available for assessing compound exposure are generally limited to whole-cell measurements. To address this gap, we recently developed a bioorthogonal chemistry-based method to assess compartment-specific compound exposure and demonstrated its use in Gram-negative bacteria. To expand the applicability of this approach, we report here novel bioorthogonal probe modalities which enable diverse probe incorporation strategies. The probes we developed utilize a cleavable thiocarbamate linker to connect localizing elements such as metabolic substrates to a cyclooctyne moiety which enables the detection of azide-containing molecules. Adducts between the probe and azide-bearing compounds can be recovered and affinity purified after exposure experiments, thus facilitating the mass-spectrometry based analysis used to assess compound exposure. The bioorthogonal system reported here thus provides a valuable new tool for interrogating compartment-specific compound exposure in a variety of biological contexts while retaining a simple and unified sample preparation and analysis workflow.

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.

Azide-tagged sphingolipids for the proteome-wide identification of C16-ceramide-binding proteins.

Ceramide plays key roles in autophagy, inflammation and apoptosis. However, little is known about the molecular mechanisms regulating its function and only a handful of cellular effectors are known for this lipid. Here we show that azide-tagged sphingolipids are powerful tools to identify ceramide targets. The combination of a protein array analysis and a mass spectrometry-based proteomic profiling successfully detects known ceramide-binding proteins and identifies others not yet reported, several of which we validated using a variety of techniques.

+Facile extraction of azide in sartan drugs using magnetized anion-exchange metal-organic frameworks prior to ion chromatography.

Quaternary amine functionalized metal-organic framework MIL-101(Cr) (MIL-101(Cr)-NMe3) was prepared as the sorbent for the magnetic solid-phase extraction (MSPE) of azide from sartan drugs before ion chromatography determination. Magnetization of MIL-101-NMe3 were achieved concurrently by adding MIL-101-NMe3 and Fe3O4@SiO2 to the sample solution under ultrasonication. The prepared Fe3O4@SiO2/MIL-101-NMe3 gave the adsorption capacity of 37.5mgg-1. The developed method had a detection limit of 0.24µgL-1 and quantitation limit of 0.79µgL-1 for azide. The relative standard deviations for the intra-day retention time and peak area were 0.52% and 0.36% (n=5), respectively. The developed method was successfully applied for the determination of azide in sartan drugs with the recoveries from 96.5% to 100.5%.

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.

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.

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.

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.

Determination of azide impurity in sartans using reversed-phase HPLC with UV detection.

A simple and robust, gradient HPLC method was developed for determination of azide ppm (µgg(-1)) levels in different sartans (irbesartan, candesartan, valsartan). The sartan was dissolved in 0.1M NaOH. Then pH was adjusted to 4.5 with 20% H3PO4 followed by dilution with water. Precipitated API was removed by filtration using 0.45µm membrane PVDF (Polyvinylidene Fluoride) membrane filter, and supernatant was analyzed by gradient elution HPLC at room temperature with Hydro RP HPLC 250×4.6mm, 4µm column and UV detection at 205nm. The best sensitivity was achieved by UV detection cell with 60mm optical path length: LOD 0.17µgg(-1) and LOQ 0.84µgg(-1) for azide. The USP requirement for maximum azide content in irbesartan is 10µgg(-1). The analytical method was validated as per International Conference on Harmonization (ICH) guidelines with respect to system precision, intraday precision (repeatability), intermediate precision (ruggedness), linearity, quantitation limit, detection limit, accuracy, standard and sample solution stability, robustness and selectivity/specificity. The method was linear in the range from LOQ (0.84µgg(-1)) to 101µgg(-1) of azide. The correlation coefficient was 0.9999 and bias on y-axis for 84µgg(-1) test concentration was 0.33%. The accuracy of the method was established based on the recovery obtained between 94.0% and 103.0% for azide. Standard and sample solutions were stable for at least 48h at room temperature and in refrigerator. The method was found to be robust for variation in column temperature (±5°C) and mobile phase flow rate (±0.2mLmin(-1)) and selective for anions such as bromide, nitrate, nitrite, formate and acetate.

Monitoring Astrocytic Proteome Dynamics by Cell Type-Specific Protein Labeling.

The ability of the nervous system to undergo long-term plasticity is based on changes in cellular and synaptic proteomes. While many studies have explored dynamic alterations in neuronal proteomes during plasticity, there has been less attention paid to the astrocytic counterpart. Indeed, progress in identifying cell type-specific proteomes is limited owing to technical difficulties. Here, we present a cell type-specific metabolic tagging technique for a mammalian coculture model based on the bioorthogonal amino acid azidonorleucine and the mutated Mus musculus methionyl-tRNA synthetaseL274G enabling azidonorleucine introduction into de novo synthesized proteins. Azidonorleucine incorporation resulted in cell type-specific protein labeling and retained neuronal or astrocytic cell viability. Furthermore, we were able to label astrocytic de novo synthesized proteins and identified both Connexin-43 and 60S ribosomal protein L10a upregulated upon treatment with Brain-derived neurotrophic factor in astrocytes of a neuron-glia coculture. Taken together, we demonstrate the successful dissociation of astrocytic from neuronal proteomes by cell type-specific metabolic labeling offering new possibilities for the analyses of cell type-specific proteome dynamics.

New potentiometric transducer based on a Mn(II) [2-formylquinoline thiosemicarbazone] complex for static and hydrodynamic assessment of azides.

A new potentiometric transducer for selective recognition of azide is characterized and developed. The PVC plasticized based sensor incorporates Mn(II) [2-formylquinoline thiosemicarbazone] complex in the presence of tri dodecyl methyl ammonium chloride (TDMAC) as a lipophilic cationic additive. The sensor displayed a near-Nernstian response for azide over 1.0×10(-2)-1.0×10(-5) mol L(-1), with an anionic slope of -55.8±0.6 mV decade(-1) and lower limit of detection 0.34 µg mL(-1). The sensor was pH independent in the range 5.5-9 and presented good selectivity features towards several inorganic anions, and it is easily used in a flow injection system and compared with a tubular detector. The intrinsic characteristics of the detector in a low dispersion manifold were determined and compared with data obtained under a hydrodynamic mode of operation. This simple and inexpensive automation, with a good potentiometric detector, enabled the analysis of ~33 samples h(-1) without requiring pre-treatment procedures. The proposed method is also applied to the analysis of trace levels of azide in primer mixtures. Significantly improved accuracy, precision, response time, stability and selectivity were offered by these simple and cost-effective potentiometric sensor compared with other standard techniques. The method has the requisite accuracy, sensitivity and precision to determine azide ions.

An enzymatic method for determination of azide and cyanide in aqueous phase.

A halohydrin dehalogenase (HHDH-PL) from Parvibaculum lavamentivorans DS-1 was characterized and applied to determine azide and cyanide in the water. In this methodology, HHDH-PL catalysed azide and cyanide to react with butylene oxide and form corresponding ß-substituted alcohols 1-azidobutan-2-ol (ABO) and 3-hydroxypentanenitrile (HPN) that could be quantitatively detected by gas chromatograph. The detection calibration curves for azide (R(2)=0.997) and cyanide (R(2)=0.995) were linear and the lower limits of detection for azide and cyanide were 0.1 and 0.3mM, respectively. Several other nucleophiles were identified having no effect on the analysis of azide and cyanide, excepting nitrite which influenced the detection of cyanide. This was the first report of a biological method to determine the inorganic azide and cyanide by converting them to the measurable organics.

Application of ethidium bromide monoazide for quantification of viable and dead cells of Salmonella enterica by real-time loop-mediated isothermal amplification.

A rapid and efficient method for quantification and discrimination of Salmonella enterica ser. Enteritidis between viable and dead cells killed by heat was developed using ethidium bromide monoazide (EMA) in combination with a real-time loop amplified (Rti-LAMP) DNA assay. The use of 8.0 µg/ml or less of EMA did not inhibit DNA amplification in Rti-LAMP assays derived from viable cells. However, 8.0 µg/ml of EMA notably inhibited DNA amplification and significantly increased the Tp values with dead cells. When the DNA from 2000 viable CFU was subjected to EMA-Rti-LAMP the resulting Tp value was 13 min. In contrast, the DNA from 2000 CFU completely heat destroyed CFU still yielded a Tp value, which was greatly increased to 33.1 min. When the DNA from viable plus heat killed CFU at a ratio of 7:1993 was subjected to EMA-Rti-LAMP, the resulting Tp value was 19.3 min, which was statistically identical (P<0.05) to the Tp value of 19.9 min. obtained with the DNA from only 7 viable CFU. These results indicate that even though 2000 dead cells yielded a Tp value of 33.1 min., low numbers of viable cells in the presence of much higher numbers of dead cells still yielded a linear plot for enumerating viable CFU from Tp values. In addition, propidium monoazide (PMA) was found to be ineffective in distinguishing between low numbers of viable and heat killed cells of S. enterica.

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.