Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria

In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this study, we initially analyzed N-terminal domains of 169 manually reviewed bacterial GBEs based on hidden Markov models. A previously unreported group of GBEs (Type 3) with around 100 amino acids ahead of the N1 domains was identified. Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla, with the shorter, Type 2 GBEs predominantly found in Gram-positive species, while the longer Type 1 GBEs are found in Gram-negative species. Several in vitro studies have linked N1 domain with transfer of short oligosaccharide chains during glycogen formation, which could lead to small and compact glycogen structures. Compact glycogen degrades more slowly and, as a result, may serve as a durable energy reserve, contributing to the enhanced environmental persistence for bacteria. We were therefore interested in classifying GBEs based on their N-terminal domain via large-scale sequence analysis. In addition, we set to understand the evolutionary patterns of different GBEs through phylogenetic analysis at species and sequence levels. Three-dimensional modeling of GBE N-termini was also performed for structural comparisons. A further study of 9,387 GBE sequences identified 147 GBEs that might belong to a possibly novel group of Type 3 GBE, most of which fall into the phylum of Actinobacteria. We also attempted to correlate glycogen average chain length (ACL) with GBE types. However, no significant conclusions were drawn due to limited data availability. In sum, our study systematically investigated bacterial GBEs in terms of domain organizations from evolutionary point of view, which provides guidance for further experimental study of GBE N-terminal functions in glycogen structure and bacterial physiology.

The application of on-line two-dimensional liquid chromatography (2DLC) in the chemical analysis of herbal medicines

Herbal medicines are complicated chemical systems containing hundreds of small molecules of various polarities, structural types, and contents. Thus far, the chromatographic separation of herbal extracts is still a big challenge. Two-dimensional liquid chromatography (2DLC) has become an attractive separation tool in the past few years. Particularly, a lot of attention has been paid to on-line 2DLC. In this review, we aim to give an overview on applications of on-line 2DLC in the chemical analysis of herbal medicines since 2010. Firstly, classification and general configurations of on-line 2DLC were briefly introduced. Then, we summarized main applications in herbal medicines of heart-cutting 2DLC (LC-LC), comprehensive 2DLC (LC × LC), and their combinations, with emphasis on LC × LC. Mass spectrometry is the most popular detector coupled with 2DLC, which allows sensitive and accurate structural characterization of herbal compounds. Finally, future developments in on-line 2DLC techniques were also discussed.

Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence

Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.

Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells

We developed a novel strategy for ATP detection in vitro and imaging in living cells based on integrating proximity hybridization-induced strand displacement and metal ion-dependent DNAzyme recycling amplification. Four DNA oligonucleotides were used in the sensing system including two aptamer probes, enzymatic sequences and FAM-linked substrate strands. Upon the addition of ATP, the proximity binding of two aptamers to ATP led to the release of the enzymatic sequences, which hybridized with the FAM-linked substrate strand on the graphene oxide (GO) surface to form the ion-dependent DNAzyme. Subsequent catalytic cleavage of the DNAzyme by the corresponding metal ions results in recycling of the enzymatic sequences and cyclic cleavage of the substrate strand, liberating many short FAM-linked oligonuleotide fragments separated from the GO surface, which results in fluorescence enhancement due to the weak affinity of the short FAM-linked oligonuleotide fragment to GO. The amount of produced short FAM-linked oligonuleotide fragments is positively related to the concentration of ATP. This means that one target binding could result in cleaving multiplex fluorophore labelled substrate strands, which provided effective signal amplification. The vivo studies suggested that the nanoprobe was efficiently delivered into living cells and worked for specific, high-contrast imaging of target ATP. More importantly, this target-responsive nanoscissor model is an important approach for intracellular amplified detection and imaging of various analytes by selecting appropriate affinity ligands.

A novel strategy for ATP imaging was developed based on proximity binding-induced strand displacement and metal ion-dependent DNAzyme recycling.

A robust fluorescent probe for detection of telomerase activityin vitroand imaging in living cellsviatelomerase-triggering primer extension to desorb DNA from graphene oxide

A novel strategy for telomerase imaging was developed based on telomerase-triggering primer extension to desorb fluorophore labeled DNA from graphene oxide.

Ionic liquids-ultrasound based efficient extraction of flavonoid glycosides and triterpenoid saponins from licorice

Flavonoid glycosides and triterpenoid saponins are the main chemical constituents of licorice. In this study, an ionic liquids-ultrasound based extraction (IL-UAE) method was established to simultaneously extract liquiritin (LQ), liquiritin apioside (LA), isoliquiritin (ILQ), isoliquiritin apioside (ILA) and glycyrrhizic acid (GA) from licorice. A series of 1-alkyl-3-methylimidazolium ILs with different anions and alkyl chain lengths of cations were investigated and compared, and 1-butyl-3-methylimidazolium acetate ([C₄MIM]Ac) was finally selected as the extractant. The extraction parameters of the IL-UAE procedure were optimized, and the established method was validated in linearity, stability, precision, repeatability and recovery. The IL-UAE approach exhibited much higher extraction efficiency comparing with conventional UAE, and needed shorter extraction time and smaller solvent to solid ratio comparing with the pharmacopoeia method. In addition, the microstructures of licorice powders were observed before and after extraction with help of a scanning electron microscope (SEM) in order to explore the extraction mechanism. The results suggested that ILs as green solvents were effective for extraction of flavonoid glycosides and triterpenoid saponins from licorice.

An ionic liquids-ultrasound based method for efficient extraction of flavonoid glycosides and triterpenoid saponins from licorice was established.

Accurate quantification of 5-Methylcytosine, 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxylcytosine in genomic DNA from breast cancer by chemical derivatization coupled with ultra performance liquid chromatography- electrospray quadrupole time of flight mass spectrometry analysis

The DNA demethylation pathway has been discovered to play a significant role in DNA epigenetics. This pathway removes the methyl group from cytosine, which is involved in the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) by ten-eleven translocation (TET) proteins. Then, 5-hmC can be iteratively oxidized to generate 5-formylcytosine (5-foC) and 5-carboxylcytosine (5-caC). However, 5-hmC, 5-foC, and 5-caC are hardly detected due to their low content. In this study, we have developed a LC-HRMS method coupled with derivatization to accurately and simultaneously quantify 5-mC levels, along with its oxidation products in genomic DNA. Derivatization was carried out using 4-dimethylamino benzoic anhydride, which has been shown to improve separation and enhance the detection sensitivity. Finally, we successfully applied this method towards the quantification of 5-mC, 5-hmC, 5-foC, and 5-caC in genomic DNA isolated from both human breast cancer tissue and tumor-adjacent normal tissue. We show that 5-foC and 5-caC are increased in tumor tissue. In addition, the levels of 5-mC, 5-hmC, 5-foC, and 5-caC measured in tumor tissue versus tumor-adjacent tissue were found to be distinct among different classifications. This suggests that cytosine modifiers could be used as potential biomarkers for determining the stage of development of breast cancer, as well as prognosis.

Enhanced detection of amino acids in hydrophilic interaction chromatography electrospray tandem mass spectrometry with carboxylic acids as mobile phase additives

Liquid chromatography coupled with mass spectrometry technique has been widely used in the analysis of biological targets such as amino acids, peptides, and proteins. In this work, eight common single carboxylic acids or diacids, which contain different pKa have been investigated as the additives to the analysis of amino acids. As the results, carboxylic acid additive can improve the signal intensity of acidity amino acids such as Asp and Glu and the chromatographic separation of basic amino acids such as Arg, His, and Lys. In particular, the diacids have better performance than single acids. The proposed mechanism is that the diacid has hydrogen bond interaction with amino acids to reduce their polarity/amphiprotic characteristics. Besides, oxalic acid has been found having better enhancement than phthalic acid by overall consideration. Therefore, we successfully quantified the 15 amino acids in Sepia bulk pharmaceutical chemical by using oxalic acid as the additive.

Metoclopramide nasal spray in vitro evaluation and in vivo pharmacokinetic studies in dogs

Metoclopramide (MCP) can effectively alleviate motion sickness-caused nausea and vomiting. Nasal administration offers the greatest patient compliance. It is suitable for self-administration and offers rapid and complete absorption, no first-pass effects and high bioavailability. In the present study, a MCP nasal spray was prepared and evaluated in vitro and in vivo. Nasal cilia toxicity of Bufo toads was used to screen the preservative types and concentrations. Rabbit nasal mucosa was used to evaluate the mucosa permeability of different MCP nasal sprays with different penetration enhancers and preservative. A three-period crossover trial was then carried out in beagle dogs with three different MCP dosage forms: nasal sprays, oral tablets and intramuscular (IM) solution. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed to measure dog plasma MCP, and pharmacokinetic parameters were calculated. The results of ciliatoxicity and permeation study showed that 0.03% methyl paraben lacking penetration enhancers was optimal. Compared to control IM, the bioavailability of oral tablets of MCP was 24.9%, while that of nasal spray was 62.3%. Meanwhile time-to-maximal plasma concentration (T_max) of nasal spray was significantly shorter than that of oral tablets. In conclusion, MCP nasal spray prepared here is safe with minimal ciliatoxicity, rapid onset and high relative bioavailability.

Investigation of the formation of the [2(iohexol) + Mg]2+ complex and its fragmentation in electrospray ionization tandem mass spectrometry

RATIONALE

Mass spectrometry has been developed as one of the common tools for the analysis of the organometallic systems in the gas phase over decades. The study of the fragmentation of organics-metal complexes has attracted much attention since the interesting dissociation pathways exhibited by these compounds are usually different from the protonated analogues.

METHODS

In this work, iohexol complexed with different dications such as Mg²⁺ , Cu²⁺ and Zn²⁺ have been investigated by electrospray ionization (ESI) tandem mass spectrometry. Additionally, deuterium-labeling experiments and an analogue of iohexol were utilized to confirm the reaction mechanisms. A computational chemistry method was used to identify the coordination conformation between iohexol and metal ions in the gas phase. UV detection was also used to identify the interaction between iohexol and metal ions in the liquid phase.

RESULTS

A special gas-phase open-loop reaction of iohexol induced by Mg²⁺ , leading to the formation of [iohexol + Mg - H - HI - C₃ H₄ O]⁺ , was observed in the collision-induced dissociation of [2(iohexol) + Mg]²⁺ complexes. Moreover, theoretical calculation shows the proposed coordination configuration of iohexol/Mg²⁺ complexes. The Mg²⁺ could have tetrahedral coordination with two iohexol molecules.

CONCLUSIONS

The percent study is a case for better understanding the formation of a typical organic/metal complex and its gas-phase fragmentation reaction. In addition, it provides useful information for researchers working on analysis or structural elucidation of complicated compounds which contain the iohexol analogues. Copyright © 2016 John Wiley & Sons, Ltd.

Hydrophilic Interaction Liquid Chromatography/Mass Spectrometry: An Attractive and Prospective Method for the Quantitative Bioanalysis in Drug Metabolism

During the development, dosage optimization and safety evaluation of a drug, rapid and precise monitoring of administered drug and/or its metabolites in biological samples including blood, plasma, serum, tissues and saliva are vital. As drug biotransformation produces more hydrophilic metabolites for the enhancement of drug elimination, which is often a challenge for traditional reversed-phase liquid chromatography (RPLC) separation. Because hydrophilic interaction liquid chromatography (HILIC) is capable of retaining polar compounds and readily compatible with mass spectrometry (MS), HILIC has been used as a complementary separation technique to RPLC for analysis of polar metabolites, especially polar drugs and their metabolites. This review covers core aspects of HILIC-MS/MS method and overall profile of its application in analysis of drug and/or its metabolites. The emphasis of this paper has been placed on the applications of HILIC-MS/MS method in quantitative bioanalysis of drugs alone or along with their metabolites in drug metabolism studies in recent years. As a fundamental and critical step of bioanalytical method, conventional sample preparation techniques of biological matrices for the HILIC-MS/MS analysis of drugs and/or their metabolites are also briefly featured.

Phenylboronic acid modified solid-phase extraction column: Preparation, characterization, and application to the analysis of amino acids in sepia capsule by removing the maltose

Maltose, a common auxiliary material of pharmaceutical preparation, may disturb the analysis of total amino acids in sepia capsule by aldolization. Therefore, it is necessary to remove the maltose through a convenient method. In this work, a phenylboronic acid modified solid-phase extraction column has been synthesized and used to remove the maltose. The materials were synthesized by one step "thiol-ene" reaction and the parameters of the column such as absorption capacity, recovery, and absorption specificity have been investigated. The results showed the column (0.5 cm of length × 0.5 cm of inner diameter) can absorb 4.6 mg maltose with a linear absorption and absorption specificity. Then this technique was applied in the quantification of amino acids in sepia capsule. After the optimization of the method, four kinds of amino acids, which were the most abundant, were quantified by high-performance liquid chromatography with diode array detection. The amounts of the four kinds of amino acids are 1.5∼2 times more than that without the treatment of solid-phase extraction column, which almost overcomes the influence of the maltose. All the results indicate that the phenylboronic acid modified solid-phase extraction column can successfully help to accurately quantify the total amino acids in sepia capsule.

Functionalized poly (ionic liquid) as the support to construct a ratiometric electrochemical biosensor for the selective determination of copper ions in AD rats

An efficient ratiometric electrochemical biosensor for Cu²⁺ determination was constructed using dual hydroxyl-functionalized poly (ionic liquid) (DHF-PIL) as the catalyst support. The DHF-PIL exhibited typical macroporous structure, which provided a high surface area of 39.31m²/g for the sufficient loading of biomolecules. The specific recognition of Cu²⁺ was accomplished by employing neurokinin B (NKB) for the first time, which could bind to Cu²⁺ to form a [Cu^II(NKB)₂] complex with high specificity. Meanwhile, a common redox mediator, 2, 2'-Azinobis-(3-ethylbenzthiazoline-6-sulfonate) (ABTS) was modified into DHF-PIL by electrostatic interactions to act as an inner reference molecule, which provided a built-in correction for environmental effects and improving the detection accuracy. With this strategy, the developed electrochemical biosensor was capable of determining Cu²⁺ with a linear range between 0.9 and 36.1μM and low detection limit (LOD) and quantification limit (LOQ) of 0.24 and 0.6μM, respectively. The sensor also displayed a satisfactory selectivity against a series of interferences in the brain, including metal ions, amino acids and other endogenous compounds. Accordingly, the present biosensor was successfully applied to evaluate Cu²⁺ levels in normal and AD rats.

A sensitive sandwich-type electrochemical aptasensor for thrombin detection based on platinum nanoparticles decorated carbon nanocages as signal labels

In this work, a novel and sensitive sandwich-type electrochemical aptasensor has been developed for thrombin detection based on platinum nanoparticles (Pt NPs) decorated carbon nanocages (CNCs) as signal tags. The morphological and compositional of the Pt NPs/CNCs were examined using transmission electron microscopy, X-ray diffraction, and Raman spectroscopy. The results showed that the Pt NPs with about 3-5nm in diameter were well dispersed on the surface of CNCs. The thiolated aptamer was firstly immobilized on the gold electrode to capture the thrombin molecules, and then aptamer functionalized Pt NPs/CNCs nanocomposites were used to fabricate a sandwich sensing platform. Then, the high-content Pt NPs on carbon nanocages acting as hydrogen peroxide-mimicking enzyme catalyzed the reduction of H2O2, resulting in significant electrochemical signal amplification. Differential pulse voltammetry is employed to detect thrombin with different concentrations. Under optimized conditions, the approach provided a good linear response range from 0.05 pM to 20nM with a low detection limit of 10fM. This Pt NPs/CNCs-based aptasensor shows good precision, acceptable stability and reproducibility, which provided a promising strategy for electrochemical aptamer-based detection of other biomolecules.

Metabolite profiles of ginsenosides Rk1 and Rg5 in zebrafish using ultraperformance liquid chromatography/quadrupole-time-of-flight MS

BACKGROUND

In the present study, metabolite profiles of ginsenosides Rk1 and Rg5 from red ginseng or red notoginseng in zebrafish were qualitatively analyzed with ultraperformance liquid chromatography/quadrupole-time-of-flight MS, and the possible metabolic were pathways proposed.

METHODS

After exposing to zebrafish for 24 h, we determined the metabolites of ginsenosides Rk1 and Rg5. The chromatography was accomplished on UPLC BEH C18 column using a binary gradient elution of 0.1% formic acetonitrile-0.1% formic acid water. The quasimolecular ions of compounds were analyzed in the negative mode. With reference to quasimolecular ions and MS2 spectra, by comparing with reference standards and matching the empirical molecular formula with that of known published compounds, and then the potential structures of metabolites of ginsenosides Rk1 and Rg5 were acquired.

RESULTS

Four and seven metabolites of ginsenoside Rk1 and ginsenoside Rg5, respectively, were identified in zebrafish. The mechanisms involved were further deduced to be desugarization, glucuronidation, sulfation, and dehydroxymethylation pathways. Dehydroxylation and loss of C-17 residue were also metabolic pathways of ginsenoside Rg5 in zebrafish.

CONCLUSION

Loss of glucose at position C-3 and glucuronidation at position C-12 in zebrafish were regarded as the primary physiological processes of ginsenosides Rk1 and Rg5.

A novel label-free and enzyme-free electrochemical aptasensor based on DNA in situ metallization

In this work, we presented a novel label-free and enzyme-free electrochemical aptasensor based on DNA in situ silver metallization as effective electrochemical label. Molecular beacon 2 (MB2, Peptide nucleic acid) was first immobilized on the gold electrode (AuE) through Au-S bond. In the presence of thrombin, the thrombin binding aptamer (MB1) preferred to form thrombin/aptamer complex in lieu of aptamer-DNA duplex, resulting in the 8-17 DNAzyme liberating from the caged structure and hybridization with the MB2, the MB2 will replace and free the target thrombin when it hybridizes with MB1. The released target thrombin can participate in the next hybridization process with MB1. Eventually, each target thrombin went through many cycles, resulting in numerous MB1 confining close to the AuE, which leaded to the surface became negatively charged and allowed the absorption of silver ions on the DNA skeleton. After chemical reduction by hydroquinone, the formed silver nanoparticles could be afforded a signal trace for electrochemical stripping analysis of target thrombin. Through introducing a hybridization chain reaction to increase the DNA length, the current signal was further amplified, achieved the detection of thrombin with a linear range from 1.0×10(-16) to 1.0×10(-11) M and a detection limit of 37 aM. In addition, the signal amplification is realized without using any enzymes or sophisticated label process, and the sensing strategy is completely non-labeled. The success in the present biosensor served as a significant step towards the development of monitoring ultratrace thrombin in clinical detection.

Simultaneous determination of baicalin, oroxylin A-7-O-glucuronide and wogonoside in rat plasma by UPLC-DAD and its application in pharmacokinetics of pure baicalin, Radix Scutellariae and Yinhuang granule

A novel UPLC-DAD method was developed and validated for the simultaneous determination of baicalin (baicalein-7-glucuronide, BG), oroxylin A-7-O-glucuronide (OAG) and wogonoside (WG) in rat plasma using rutin as the internal standard. Plasma samples were precipitated using acetonitrile containing 0.1% formic acid. Separation was performed on an Agilent Eclipse Plus C18 column (2.1 × 50 mm, 1.8 µm) using gradient acetonitrile and 0.2% formic acid water solution as mobile phase. The flow-rate was set at 0.4 mL/min and the eluate was detected at 275 nm. The method was linear over the ranges of 0.075-17.50, 0.050-12.60 and 0.056-14.10 µg/mL for BG, OAG and WG, respectively. The intra- and inter-day precisions were respectively <4.8% and 6.4%. All of the limits of detection of three analytes in rat plasma were 0.01 µg/mL, whereas the limits of quantification were, respectively, 0.035, 0.025 and, 0.025 µg/mL. This assay has been successfully applied to pharmacokinetics of BG, OAG and WG in rats after oral administration of Yinhuang granule (YHG) and comparative pharmacokinetics of BG in rats following oral administration of the pure BG, Radix Scutellariae (RS) or YHG. We speculate that some co-existing ingredients in RS or YHG may increase the absorption and elimination of BG in rat. This work may be helpful for the quality control of Yinhuang granule.