Determination of pyridine and adenine nucleotide metabolites in Bacillus subtilis cell extract by sweeping borate complexation capillary electrophoresis

Modified Lactoperoxidase System as a Promising Anticaries Agent: In Vitro Studies on Streptococcus mutans Biofilms

The lactoperoxidase (LPO) system shows promise in the prevention of dental caries, a common chronic disease. This system has antimicrobial properties and is part of the non-specific antimicrobial immune system. Understanding the efficacy of the LPO system in the fight against biofilms could provide information on alternative strategies for the prevention and treatment of caries. In this study, the enzymatic system was modified using four different (pseudo)halide substrates (thiocyanate, thiocyanate-iodide mixture, selenocyanate, and iodide). The study evaluated the metabolic effects of applying such modifications to Streptococcus mutans; in particular: (1) biofilm formation, (2) synthesis of insoluble polysaccharides, (3) lactate synthesis, (4) glucose and sucrose consumption, (5) intracellular NAD+ and NADH concentrations, and (6) transmembrane glucose transport efficiency (PTS activity). The results showed that the LPO-iodide system had the strongest inhibitory effect on biofilm growth and lactate synthesis (complete inhibition). This was associated with an increase in the NAD+/NADH ratio and an inhibition of glucose PTS activity. The LPO-selenocyanate system showed a moderate inhibitory effect on biofilm biomass growth and lactate synthesis. The other systems showed relatively small inhibition of lactate synthesis and glucose PTS but no effect on the growth of biofilm biomass. This study provides a basis for further research on the use of alternative substrates with the LPO system, particularly the LPO-iodide system, in the prevention and control of biofilm-related diseases.

Versatile Functional Energy Metabolism Platform Working From Research to Patient: An Integrated View of Cell Bioenergetics

Mitochondrial dysfunctions that were not discovered during preclinical and clinical testing have been responsible for at least restriction of use as far as withdrawal of many drugs. To solve mitochondrial machinery complexity, integrative methodologies combining different data, coupled or not to mathematic modelling into systems biology, could represent a strategic way but are still very hard to implement. These technologies should be accurate and precise to avoid accumulation of errors that can lead to misinterpretations, and then alter prediction efficiency. To address such issue, we have developed a versatile functional energy metabolism platform that can measure quantitatively, in parallel, with a very high precision and accuracy, a high number of biological parameters like substrates or enzyme cascade activities in essential metabolism units (glycolysis, respiratory chain ATP production, oxidative stress...) Its versatility (our platform works on either cell lines or small animals and human samples) allows cell metabolism pathways fine tuning comparison from preclinical to clinical studies. Applied here to OXPHOS and/or oxidative stress as an example, it allows discriminating compounds with acute toxic effects but, most importantly, those inducing low noise chronic ones.

Extraction and preconcentration of compounds from the l-tyrosine metabolic pathway prior to their micellar electrokinetic chromatography separation

The prominent biological effects of adrenaline (A), noradrenaline (NA) and dopamine (DA) as well as the clinical importance of their metabolites (such as dihydroxyphenylacetic acid (DOPAC), methoxy‑4-hydroxyphenyl glycol (MHPG), dihydroxyphenylglycol (DHPG), metanephrine (M), normetanephrine (NM), vanillylmandelic acid (VMA), homovanillic acid (HVA)) have forced researchers to evaluate new analytical methodologies for their isolation and preconcentration from biological samples. For this reason, the three most popular extraction techniques (dispersive liquid-liquid microextraction (DLLME), solid-phase extraction (SPE), solid-phase microextraction (SPME)) were tested. Micellar electrokinetic chromatography (MEKC) - a mode of capillary electrophoresis - with a diode array detector (DAD) was applied to assess the extraction efficiency. Next, the enrichment factor (EF) of each applied method was calculated in respect to standard mixtures of the analytes at the same concentration levels. The EF results of seven selected metabolites of biogenic amines (BAs) from urine after sample preparation procedures based on twenty-five different protocols (one DLLME, thirteen SPE and eleven SPME) were calculated and compared using hierarchical cluster analysis (HCA). The SPE as well as SPME procedures were proved to be the most effective approaches for the simultaneous extraction of the chosen compounds. Moreover, an ionic liquid (IL) - 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide - added to methanol in SPME additionally could successfully improve the extraction efficiency. It was also confirmed that the HCA approach could be considered a supportive tool in the selection of a suitable sample preparation procedure for that group of endogenous substances.

Enhanced single-cell metabolomics by capillary electrophoresis electrospray ionization-mass spectrometry with field amplified sample injection

Single-cell metabolomics provides information on the biochemical state of an individual cell and its relationship with the surrounding environment. Characterization of metabolic cellular heterogeneity is challenging, in part due to the small amounts of analytes and their wide dynamic concentration ranges within individual cells. CE-ESI-MS is well suited to single-cell assays because of its low sample-volume requirements and low detection limits. While the volume of a cell is in the picoliter range, after isolation, the typical volume of the lysed cell sample is on the order of a microliter; however, only nanoliters are injected into the CE system, with the volume mismatch limiting analytical performance. Here we developed an approach for the detection of intracellular metabolites from a single neuron using field amplified sample injection (FASI) CE-ESI-MS. Through the application of FASI, we achieved 100- to 300-fold detection limit enhancement compared to hydrodynamic injections. We further enhanced the analyte identification and quantification accuracy via introduction of two internal standards. As a result, the relative standard deviations of migration times were reduced to <5%, aiding identification. Finally, we successfully applied FASI CE-ESI-MS to the untargeted profiling of metabolites of Aplysia californica pleural sensory neurons with <50 μm diameter cell somata. As a result, twenty one neurotransmitters and metabolites have been quantified in these neurons.

Amplification of lysozyme signal detected in capillary electrophoresis using mixed polymer brushes coating with switchable properties

In this work, a mixed polymer brushes based on poly(2-methyl-2-oxazoline) (PMOXA) and poly(acrylic acid) (PAA) coated capillary with switchable protein adsorption/desorption properties was developed and applied for on-line extraction and preconcentration of lysozyme. The study of electroosmotic flow (EOF) and fluorescence microscope showed that the inner surface charge of PMOXA/PAA mixed brush coated capillary displayed the switchable behavior toward the change of pH value and ionic strength (I), and PMOXA/PAA mixed brushes coated capillary could adsorb high amounts of lysozyme at pH 7 (I = 10^-5 M), and the most of adsorbed lysozyme could then be desorbed at pH 3 (I = 10^-1 M). Subsequently, this coated capillary with switchable lysozyme adsorption/desorption ability was applied for on-line extraction and preconcentration of lysozyme during capillary electrophoresis (CE) performance. Under the process of on-line preconcentration, the detection signal (peak area) of lysozyme obtained in PMOXA/PAA coated capillary was 26 times that obtained in bare capillary under normal CE while the contour chain length of PAA was 1.56 times that of PMOXA. Moreover, the value of low detection limit (LOD) of lysozyme using above coated capillary under on-line preconcentration method reached to 4.5 × 10^-9 mg/mL, and 1 × 10⁵-fold sensitivity enhancement was realized for lysozyme as compared with the bare capillary under normal CE.

Simultaneous detection of nicotinamide adenine nucleotides and adenylate pool to quantify redox and energy states in mAb-producing CHO cells by capillary electrophoresis

Chinese hamster ovary (CHO) cells are predominant in the production of therapeutic proteins to treat various diseases. Characterization and investigation of CHO cell metabolism in a quick and simple way could boost process and cell line development. Therefore, a method to simultaneously detect seven redox- and energy-related metabolites in CHO cells by capillary electrophoresis has been developed. An on-line focusing technique was applied to improve the peak shape and resolution by using a 50 μm × 44 cm uncoated fused silica capillary. Key parameters and their interactions were investigated by design of experiments (DoE) and optimized conditions were determined by desirability function as follows: 24 °C, 95 mM, and pH 9.4 of BGE. The method was validated to ensure sensitivity, linearity, and reproducibility. The limits of detection (LODs) ranged from 0.050 to 0.688 mg/L for seven metabolites, and correlation coefficients of linearity were all greater than 0.996. The relative standard deviations (RSD) of migration time and peak area were smaller than 0.872% and 5.5%, respectively, except for NADPH, and the recoveries were between 97.5 and 101.2%. The method was successfully applied to analyze the extracts from CHO cells under two different culture conditions. Graphical abstract.

Simultaneous determination of intracellular nucleotides and coenzymes in Yarrowia lipolytica producing lipid and lycopene by capillary zone electrophoresis

Yarrowia lipolytica is an oleaginous yeast with promise in producing terpenoids such as lycopene. Though methods for analyzing primary metabolic intermediates have been established, further work is needed to better analyze nucleotides and coenzymes. Here, we presented an optimized method for the separation of nucleotides and coenzymes in Y. lipolytica using the capillary electrophoresis. The separation of twelve metabolites including four coenzymes, five nucleotides and three nucleosides was achieved within 32min using a voltage of 15kV and 70mM sodium carbonate/hydrogencarbonate buffer with 1.0% β-CD at pH 10. The results show that the concentrations of adenosine triphosphate and nicotinamide adenine dinucleotide phosphate changed significantly between lycopene producing strain and the control, indicating that these two metabolites may be closely related with lycopene production. The optimized method provides a useful approach for future metabolic analysis of fermentation process as well as industrial strain improvement.

Design and synthesis of novel adenine fluorescence probe based on Eu(III) complexes with dtpa-bis(guanine) ligand

A novel adenine (Ad) fluorescence probe (Eu^III-dtpa-bis(guanine)) was designed and synthesized by improving experimental method based on the Eu(III) complex and dtpa-bis(guanine) ligand. The dtpa-bis(guanine) ligand was first synthesized by the acylation action between dtpaa and guanine (Gu), and the corresponding Eu(III) complex was successfully prepared through heat-refluxing method with dtpa-bis(guanine) ligand. As a novel fluorescence probe, the Eu^III-dtpa-bis(guanine) complex can detect adenine (Ad) with characteristics of strong targeting, high specificity and high recognition ability. The detection mechanism of the adenine (Ad) using this probe in buffer solution was studied by ultraviolet-visible (UV-vis) and fluorescence spectroscopy. When the Eu^III-dtpa-bis(guanine) was introduced to the adenine (Ad) solution, the fluorescence emission intensity was significantly enhanced. However, adding other bases such as guanine (Gu), xanthine (Xa), hypoxanthine (Hy) and uric acid (Ur) with similar composition and structure to that of adenine (Ad) to the Eu^III-dtpa-bis(guanine) solution, the fluorescence emission intensities are nearly invariable. Meanwhile, the interference of guanine (Gu), xanthine (Xa), hypoxanthine (Hy) and uric acid (Ur) on the detection of the adenine using Eu^III-dtpa-bis(guanine) probe was also studied. It was found that presence of these bases does not affect the detection of adenine (Ad). A linear response of fluorescence emission intensities of Eu^III-dtpa-bis(guanine) at 570nm as a function of adenine (Ad) concentration in the range of 0.00-5.00×10^-5molL^-1 was observed. The detection limit is about 4.70×10^-7molL^-1.

Simultaneous quantification of energetically important metabolites in various cell types by CZE

A new CZE method was developed for the determination of 12 purine and pyrimidine nucleotides, two adenine coenzymes and their reduced forms, and acetyl coenzyme A in various cell extracts. As the concentration levels of these metabolites in living cells are low; CZE was combined with field-enhanced sample stacking. As a result, the separation conditions were optimised to achieve a suitable resolution at the relatively high sample volume provided by this on-line pre-concentration technique. The optimum BGE was 150 mM glycine buffer (pH 9.5). Samples were introduced hydrodynamically using a pressure of 35 mbar (3.5 kPa) for 25 s, and data were collected at a detection wavelength of 260 nm. An applied voltage of 30 kV (positive polarity) and capillary temperature of 25°C gave the best separation of these compounds. The optimised method was validated by determining the linearity, sensitivity and repeatability and it was successfully applied for the analysis of extracts from Paracoccus denitrificans bacteria and from stem cells.

Capillary zone electrophoresis with field enhanced sample stacking as a tool for targeted metabolome analysis of adenine nucleotides and coenzymes in Paracoccus denitrificans

The main aim of this work was to demonstrate the applicability of capillary zone electrophoresis in combination with field enhanced sample stacking in targeted metabolome analyses of adenine nucleotides--AMP, ADP, ATP, coenzymes NAD(+), NADP(+) and their reduced forms in Paracoccus denitrificans. Sodium carbonate/hydrogencarbonate buffer (100 mM, pH 9.6) with the addition of beta-CD at a concentration of 10 mM was found to be an effective BGE for their separation within 20 min. Besides this, special attention was paid to the development of the procedure for the extraction of specific metabolites from the bacterium P. denitrificans. This procedure was not only optimised to achieve the highest metabolite yields but also to obtain a sample that was fully compatible with the online preconcetration strategy used. The developed methodology was finally applied in a study of the bacterium P. denitrificans at various stages of the active respiratory chain.

Metabolomics for biotransformations: Intracellular redox cofactor analysis and enzyme kinetics offer insight into whole cell processes

For redox reactions catalyzed by microbial cells the analysis of involved cofactors is of special interest since the availability of cofactors such as NADH or NADPH is often limiting and crucial for the biotransformation efficiency. The measurement of these cofactors has usually been carried out using spectrophotometric cycling assays. Today LC-MS/MS methods have become a valuable tool for the identification and quantification of intracellular metabolites. This technology has been adapted to measure all four nicotinamide cofactors (NAD, NADP, NADH, and NADPH) during a whole cell biotransformation process catalyzed by recombinant Escherichia coli cells. The cells overexpressing an alcohol dehydrogenase from Lactobacillus brevis were used for the reduction of methyl acetoacetate (MAA) with substrate-coupled cofactor regeneration by oxidation of 2-propanol. To test the reliability of the measurement the data were evaluated using a process model. This model was derived using the measured concentrations of reactants and cofactors for initiation as well as the kinetic constants from in vitro measurements of the isolated enzyme. This model proves to be highly effective in the process development for a whole cell redox biotransformation in predicting both the right concentrations of cofactors and reactants in a batch and in a CSTR process as well as the right in vivo expression level of the enzyme. Moreover, a sensitivity analysis identifies the cofactor regeneration reaction as the limiting step in case for the reduction of MAA to the corresponding product (R)-methyl 3-hydroxybutyrate. Using the combination of in vitro enzyme kinetic measurements, measurements of cofactors and reactants and an adequate model initiated by intracellular concentrations of all involved reactants and cofactors the whole cell biotransformation process can be understood quantitatively.

Combination of on-chip field amplification and bovine serum albumin sweeping for ultrasensitive detection of green fluorescent protein

We report a highly effective on-chip preconcentration method by combining field-amplified sample injection (FASI) and bovine serum albumin (BSA) sweeping for ultrasensitive detection of green fluorescent protein (GFP) on a simple cross-channel microchip device. With the formation of a stagnant sample/running buffer boundary by balancing the hydrodynamic flow and the electro-osmotic flow (EOF), GFP molecules can be continuously injected into the sample loading channel and stacked. We have also demonstrated that BSA is a very effective pseudo-stationary phase for sweeping concentration of proteins in comparison to the commonly used micelles. The combination of FASI and BSA sweeping yields a concentration factor of 3570 and a limit of detection of 8.4 pM for GFP. Using this method, we have separated GFP and GFP-insulin-like growth factor-I (GFP-IGF-I) fusion protein. The entire assay (GFP concentration, matrix elimination, and electrophoretic separation) can be completed within <5 min. Furthermore, we have successfully applied this method for the detection of GFP expression of E. coli cells and the GFP content in single E. coli cells.

Sweeping and new on-line sample preconcentration techniques in capillary electrophoresis

Sweeping is a powerful on-line sample preconcentration technique that improves the concentration sensitivity of capillary electrophoresis (CE). This approach is designed to focus the analyte into narrow bands within the capillary, thereby increasing the sample volume that can be injected, without any loss of CE efficiency. It utilizes the interactions between an additive [i.e., a pseudostationary phase (PS) or complexing agent] in the separation buffer and the sample in a matrix that is devoid of the additive used. The accumulation occurs due to chromatographic partitioning, complexation or any interaction between analytes and the additive through electrophoresis. The extent of the preconcentration is dependent on the strength of interaction involved. Both charged and neutral analytes can be preconcentrated. Remarkable improvements--up to several thousandfold--in detection sensitivity have been achieved. This suggests that sweeping is a superior and general approach to on-line sample preconcentration in CE. The focusing mechanism of sweeping under different experimental conditions and its combination with other on-line preconcentration techniques are discussed in this review. The recently introduced techniques of transient trapping (tr-trapping) and analyte focusing by micelle collapse (AFMC) as well as other novel approaches to on-line sample preconcentration are also described.

Separation of flavins and nicotinamide cofactors in Chinese hamster ovary cells by capillary electrophoresis

Simultaneous extraction, separation and quantitation of reduced nicotinamide adenine dinucleotide (NADH), reduced nicotinamide adenine dinucleotide phosphate (NADPH), flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) in Chinese Hamster Ovary (CHO) cells were investigated. The separation of flavins and nicotinamide cofactors was performed by capillary electrophoresis with laser-induced fluorescence detection at the excitation wavelength of 325 nm. The separation protocol was established by investigating the excitation wavelength, high voltage and effects of buffer nature, pH and concentration. All endogenous fluorophores riboflavin, FAD, FMN, NADH and NADPH show wide linear range of quantitation. The limits of detection for the five compounds ranged from 4.5 to 23 nM. Extraction conditions were optimized for high-efficiency recovery of all endogenous fluorophores from CHO cells. To account for the complex matrix of cell extracts, a standard addition method was used to quantify FAD, FMN, NADH and NADPH in CHO cells. The quantitative results should be useful to reveal the metabolic status of cells. The protocols for extraction, separation and quantitation are readily adaptable to normal and cancer cell lines for the analysis of endogenous fluorophores.

Quantitative profiling of nucleotides and related phosphate-containing metabolites in cultured mammalian cells by liquid chromatography tandem electrospray mass spectrometry

A method has been developed for the quantitative profiling of over twenty nucleotides and related phosphorylated species using ion-pair reversed-phase liquid chromatography hyphenated to negative ion tandem electrospray mass spectrometry. The influence of mobile phase pH and ion-pairing agent concentration were assessed to optimise separation and peak shapes. Full quantitative analysis was obtained for the nucleotides by reference to structurally related calibration standards. The developed method was applied to profile changes in nucleotides and related compounds in monolayer cultured Chinese hamster ovary (CHO) cells expressing the beta(2) adrenoceptor when exposed to pharmacological stimuli. These experiments demonstrate the potential of the LC-MS/MS method to detect changes in nucleotide drug targets as well as the simultaneous monitoring of levels of other nucleotides.

Combination of large volume sample stacking and dynamic pH junction for on-line preconcentration of weak electrolytes by capillary electrophoresis in comparison with isotachophoretic techniques

An on-line preconcentration capillary electrophoresis (CE) technique, which combines a large volume sample stacking with a dynamic pH junction technique, is introduced in this paper. This dynamic pH junction with co-electroosmotic migration is formed between sodium borate pH 9.5 and sodium phosphate pH 2.5 with 150 mM sodium dodecylsulfate (SDS). A full capillary based injection allows determination of weak acidic compounds at ppb concentration levels (achieved LOD for benzoic acid was 11 nmol L(-1)). The proposed preconcentration method was compared with ITP/ITP (LOD 120 nmol L(-1)), ITP/CZE (LOD 740 nmol L(-1)) and a simple CZE method (LOD 23,330 nmol L(-1)). The analytical potential of this method was assessed with juice test samples.

Electrochemical sensing based on redox mediation at carbon nanotubes

An electrochemical sensing platform was developed based on the integration of redox mediators and carbon nanotubes (CNT) in a polymeric matrix. To demonstrate the concept, a redox mediator Azure dye (AZU) was covalently attached to polysaccharide chains of chitosan (CHIT) and interspersed with CNT to form composite films for the amperometric determination of beta-nicotinamide adenine dinucleotide (NADH). The incorporation of CNT into CHIT-AZU matrix facilitated the AZU-mediated electrooxidation of NADH. In particular, CNT decreased the overpotential for the mediated process by an extra 0.30 V and amplified the NADH current by approximately 35 times (at -0.10 V) while reducing the response time from approximately 70 s for CHIT-AZU to approximately 5 s for CHIT-AZU/CNT films. These effects were discussed in terms of the AZU/CNT synergy, which improved charge propagation through the CHIT-AZU/CNT matrix. The concept of CNT-facilitated redox mediation in polymeric matrixes has a potential to be of general interest for expediting redox processes in electrochemical devices such as sensors, biosensors, and biological fuel cells and reactors.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips

Poor sensitivity is considered to be one of the major limitations of electrophoretic separation methods, particularly when compared to traditional liquid chromatographic techniques. To address this issue, various in-line preconcentration techniques have been developed over the past 15 years, ranging in power and complexity, and there are now a number of well understood approaches routinely capable of providing a 10,000- to 100,000-fold increase in sensitivity, as well as several that can be pushed above a million. Furthermore, these have been achieved with particularly troublesome and often difficult samples, such as those having high salinity from a biological or environmental origin. This review will discuss the most common methods for improving the sensitivity of CE, CEC and microchip version of these, with particular attention to those approaches developed over the last five years.

Development of a NACE method for simultaneous measurement of three adenosine monophosphate isomers in biomimicking prebiotic synthesis without sample pretreatment

A practical NACE method was developed for simultaneous determination of three adenosine monophosphate (AMP) isomers. Separation of three AMP isomers was achieved using 200 mM Tris/H(3)BO(3) in acetontrile/water (2:1 v/v) at pH* 10.0 as the running buffer and +25 kV as the applied voltage over a bare fused-silica capillary of 50 microm id x 375 microm od x 54.5 cm (46 cm to the detector window). At 260 nm, the calibration curves were linear in the range of 1-100 microg/mL. The detection limits were less than 0.70 microg/mL. The recovery ranged from 94.5 to 106.4%. The intraday RSDs of the migration times were between 2.1 and 3.0%. The developed NACE method has been successfully applied for the determination of three AMP isomers in the real samples of biomimicking prebiotic synthesis reaction between N-(O,O-diisopropyl) phosphoryl amino acid and adenosine.

Determination of endogenous norepinephrine levels in different chambers of the rat heart by capillary electrophoresis coupled with amperometric detection

Capillary electrophoresis with end-column amperometric detection (CE-EC) was used to determine the regional distribution of norepinephrine (NE) in the hearts of sympathetically innervated (control) and chemically sympathectomized rats. Key features of the method are (i) the sample preparation and clean-up step that involved the application of off-line solid phase extraction (SPE) with a 95% NE recovery and (ii) the use of a diamond microelectrode for detection. NE was quantified in the left and right ventricle, the ventricular septum, and the left and right atrium. The NE concentration in the atria was three to five times higher than in the ventricles and ventricular septum of control rats. Basal NE levels in the left and right ventricle and the ventricular septum were reduced to below the detection limit (0.034 microg/g tissue) in tissues treated with the neurotoxin, 6-hydroxydopamine (6-OHDA), while only a moderate reduction was observed in the left and right atrium. Importantly, the diamond microelectrode provided low and stable background current and low peak-to-peak noise <or=0.65 pA at a detection potential of +0.86 V versus Ag/AgCl. A reproducible electrode response was observed for multiple injections of tissue homogenates with minimal response attenuation due to electrode fouling.

Application of CE for determination of DNA base composition

DNA base composition expressed as mol% of guanine plus cytosine (% GC) or GC content is a key parameter of bacterial taxonomy and genomic analyses. Direct chemical determination methods such as HPLC as well as indirect methods based on physical properties of deoxyribonucleic acid (DNA), melting point (T(m)), and buoyant density (B(d)) have been conventionally applied to determine the GC content. However, these methods require relatively large amounts of sample DNA, time, and labor. We have developed a protocol to determine the GC content by fine separation of nucleosides with CZE. Genomic DNAs with known GC content from 23 bacterial strains were determined by CE at the optimized conditions of 27 degrees C, 20 kV in 50 mM of NaHCO(3) (pH 9.0) and 70 mM SDS added. Nucleosides from <1 microg of DNA hydrolyzed with nuclease-P1 and bacterial alkaline phosphatase were separated in a 75 microm wide and 80 cm long silica capillary. The nucleoside peak areas were determined at 254 nm in less than 12 min. The CE-based determination of GC content requires only small amounts of DNA, and thus should be applicable to environmental genomics (metagenomics), as >90% of environmental micro-organisms are nonculturable and produce only small amounts of genomic DNA.

Determination of adenine and pyridine nucleotides in glucose-limited chemostat cultures of Penicillium simplicissimum by one-step ethanol extraction and ion-pairing liquid chromatography

Under specific conditions Penicillium simplicissimum excretes large amounts of organic acids, mainly citrate. As the energetic status of the hyphae might play a role in that respect, we developed a method for the determination of adenine (adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate) and pyridine (nicotinamide adenine dinucleotide and reduced nicotinamide adenine dinucleotide (NADH)) nucleotides in hyphae of P. simplicissimum. An optimum separation of the five compounds in less than 15 min was possible on a C-8 column, utilizing 50 mM aqueous triethylamine-buffer (pH 6.5) and acetonitrile as mobile phase; detection was performed at 254 nm. With the exception of NADH, which could not be determined accurately due to stability problems, the method was sensitive (LOD < or = 0.7 ng on-column), repeatable (sigma(rel) < or = 4.4%), accurate (recovery rates between 97.9 and 104.9%), and precise (intraday variation < or = 9.4%, interday variation < or = 6.2 %). For an optimum extraction of the nucleotides the chemostat samples were directly placed into hot (90 degrees C) 50% ethanol, and shaken for 10 min, followed by evaporation of the solvent and a solid phase extraction cleanup of the redissolved aqueous samples. With this method the nucleotide concentrations in hyphae from a glucose-limited chemostat culture and the respective energy charge were determined. Additionally, the effect of the time lag between sampling and extraction and the effect of a glucose pulse on nucleotide concentrations were determined.

Improved properties of the non-covalent coating with N,N-didodecyl-N, N-dimethylammonium bromide for the separation of basic proteins by capillary electrophoresis with acidic buffers in 25μm capillaries

Capillaries (25microm I.D.) treated with the double-alkyl-chain cationic surfactant N,N-didodecyl-N, N-dimethylammonium bromide (DDAB) in an improved coating procedure were used for separation of four basic proteins in volatile buffers (ammonium acetate and ammonium hydroxyacetate) as well as in a non-volatile buffer (sodium phosphate) at pH 4. The DDAB coating was stable enough to, without recoating, permit consecutive separations of the proteins up to 9h with good precisions in peak areas (RSD=1.1%) and migration times and with high apparent efficiencies (over 1 million theoretical plates/m) in the presence of a strong anodic electroosmosis. Adsorption of the proteins onto the capillary surface, which in previous studies was found to give a certain contribution to zone broadening, was eliminated with the new modified coating method. Complex formation between the proteins and phosphate buffer was studied and confirmed, and it is proposed that slow protein-buffer component interactions are the main contributions to zone broadening in protein separations by CE.

Analysis of Strychnos alkaloids in traditional Chinese medicines with improved sensitivity by sweeping micellar electrokinetic chromatography

The application of an on-line sweeping preconcentration method in micellar electrokinetic chromatography (MEKC) for the determination of Strychnos alkaloids, namely strychnine and brucine, has been investigated in this work. After experimental optimizations, the best separation was achieved in 50 mmol l(-1) H3PO4 (pH 2.0) containing 100 mmol l(-1) SDS and acetonitrile in a ratio of 4:1 (v/v), with an applied voltage of -20 kV at 20 degrees C. The sample matrix consisted of 100 mmol l(-1) H3PO4 (pH 2.0), and sample introduction was performed at 0.5 psi for 270 s, with photodiode array detection at 203 nm. Compared with the conventional MEKC injection method, up to 100-fold improvement in concentration sensitivity was achieved in terms of peak height by using this sweeping injection technique. In the method, the compound berberine was used as the internal standard for the improvement of the experimental reproducibility. The calibration curve was linear over a range of 0.5-15 microg ml(-1) for both strychnine and brucine, with a correlation coefficient of 0.998 and 0.997, respectively. The detection limits (S/N=3:1) for strychnine and brucine were 0.05 and 0.07 microg ml(-1), respectively. The sweeping-MEKC method has been successfully applied to the analysis of strychnine and brucine in Strychnos nux-vomica L. and its Chinese medicinal preparations.

Carbon nanotube-chitosan system for electrochemical sensing based on dehydrogenase enzymes

Multiwalled carbon nanotubes (CNT) were solubilized in aqueous solutions of a biopolymer chitosan (CHIT). The CHIT-induced solubilization of CNT facilitated their manipulations, including the modification of electrode surfaces for sensor and biosensor development. The colloidal solutions of CNT-CHIT were placed on the surface of glassy carbon (GC) electrodes to form robust CNT-CHIT films, which facilitated the electrooxidation of NADH. The GC/CNT-CHIT sensor for NADH required approximately 0.3 V less overpotential than the GC electrode. The susceptibility of CHIT to chemical modifications was explored in order to covalently immobilize glucose dehydrogenase (GDH) in the CNT-CHIT films using glutaric dialdehyde (GDI). The stability and sensitivity of the GC/CNT-CHIT-GDI-GDH biosensor allowed for the interference-free determination of glucose in the physiological matrix (urine). In pH 7.40 phosphate buffer solutions, linear least-squares calibration plots over the range 5-300 microM glucose (10 points) had slopes 80 mA M(-1) cm(-2) and a correlation coefficient 0.996. The detection limit was 3 microM glucose (S/N = 3). The CNT-CHIT system represents a simple and functional approach to the integration of dehydrogenases and electrodes, which can provide analytical access to a large group of enzymes for wide range of bioelectrochemical applications including biosensors and biofuel cells.

Integrating metabolomics into a systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms

As an important functional genomic tool, metabolomics has been illustrated in detail in recent years, especially in plant science. However, the microbial category also has the potential to benefit from integration of metabolomics into system frameworks. In this article, we first examine the concepts and brief history of metabolomics. Next, we summarize metabolomic research processes and analytical platforms in strain improvements. The application cases of metabolomics in microorganisms answer what the metabolomics can do in strain improvements. The position of metabolomics in this systems biology framework and the real cases of integrating metabolomics into a system framework to explore the microbial metabolic complexity are also illustrated in this paper.

Two-dimensional separation system of coupling capillary liquid chromatography to capillary electrophoresis for analysis of Escherichia coli metabolites

A two-dimensional (2-D) separation system of coupling chromatography to electrophoresis was developed for profiling Escherichia coli metabolites. Capillary liquid chromatography (LC) with a monolithic silica-octadecyl silica column (500 x 0.2 mm ID) was used as the first dimension, from which the effluent fractions were further analyzed by capillary electrophoresis (CE) acting as the second dimension. Field-enhanced stacking was selectively employed as a concentration strategy to interface the two dimensions, which proved to be beneficial for the detection of metabolites. An artificial sample containing 118 standards, some of which lack chromophores or have weak UV absorbance, was used to optimize the 2-D separation system. Under the optimum conditions, 63 components in the artificial sample having absorbance at 254 nm could be well resolved and detected. The utility of the system was demonstrated by comprehensive analysis of E. coli metabolites. Comparing with the previous 2-D separation system we published in Anal. Chem. 2004, 76, 1419-1428, using a longer monolithic column in the first dimension improved the separation efficiency and offered the possibility of increasing the injection volume without compromising the separation efficiency. In the second dimension, field-enhanced stacking was used to improve the concentration sensitivity of the metabolites, and more metabolites in E. coli cell extract were detected and identified using the developed 2-D separation system. In addition, preliminary investigation for future CE-mass spectrometry coupling was also made in the study by using volatile buffers in the capillary LC and CE techniques.

Analysis of the disaccharides derived from hyaluronic acid and chondroitin sulfate by capillary electrophoresis with sample stacking

CE conditions for monitoring the unsaturated disaccharides of hyaluronic acid (di-HA) and chondroitin sulfate (di-CS) using an alkaline tetraborate buffer, electrokinetic sample injection, and UV absorption detection at 232 nm are reported. Separations were performed in an uncoated fused-silica capillary having reversed polarity and reversed electroosmosis generated with the addition of CTAB to the buffer. The influence of various separation parameters, including the concentration of CTAB, buffer pH, concentration of tetraborate, and applied voltage, on the resolution of the two disaccharides was investigated. Baseline separation was obtained with 25 mM tetraborate at pH 10.0 and having 0.05 mM CTAB. Chloride and phosphate in the sample are beneficial for the stacking of the disaccharides, with di-HA forming a much sharper peak than di-CS. Using samples prepared in 25 mM Tris-HCl (pH 7.5) and electrokinetic injection at the cathode at -10 kV for 40 s, linear relationships between the corrected peak area and the concentration of the disaccharides have been found in the ranges of 1.0-400.0 and 0.1-1.0 microg/mL (0.2-1.0 microg/mL for di-CS), with correlation coefficients being >0.9933 in all cases. The RSDs of detection times and corrected peak areas were between 1.13-1.24 and 1.57-2.13%, respectively. Applied to human serum samples that were prepared by ethanol precipitation and depolymerization of the two polysaccharides with chondroitinase ABC reveals comigration of endogenous compounds with di-HA and a sample-dependent detection time. The di-HA content in the serum sample can be estimated via subtraction of the blank peak that is obtained without enzymatic hydrolysis.

Micro-separation toward systems biology

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Human red blood cells targeted metabolome analysis of glycolysis cycle metabolites by capillary electrophoresis using an indirect photometric detection method

A capillary electrophoretic (CE) method with UV indirect spectrophotometric detection for determination of the main compounds of glycolysis in human erythrocytes has been elaborated. Blood samples for electrophoretic analysis were prepared by isolation of erythrocytes, lysis of the cells by heating in double-distilled water and subsequent ultrafiltration with a centrifuge equipped with filter devices: Mr cut off 5000. Using 20 mM 2,6-pyridinedicarboxylic acid (PDC) as a highly UV absorbing carrier electrolyte and 4 mM cetyltrimetylammonium bromide (CTAB), at the resulting pH 12.3, nine of the glycolysis intermediates were separated and characterized. The repeatability and linearity of the method was assessed with percent relative standard deviation (%R.S.D.) for migration time ranging from 0.3 to 1.9% and correlation coefficients of 0.991-0.999 for the studied concentration range. Limits of detection (LOD) for the analyzed metabolites were in the range of 6.25 x 10(-6) to 5.0 x 10(-5) M. The optimized CE method was used to compare metabolome content of red blood cells of 22 healthy volunteers. Mean metabolite concentrations in erythrocytes ranged from 49.6 microM for fructose-6-phosphate (F-6-P) to 3.1 mM for 2,3-diphospho-D-glyceric acid (2,3-DPG). The method can be readily applied in clinical, pathophysiological and epidemiological studies.

Quantitation of nicotinamide and serotonin derivatives and detection of flavins in neuronal extracts using capillary electrophoresis with multiphoton-excited fluorescence

Capillary electrophoresis (CE) with multiphoton-excited fluorescence detection (CE-MPE) allows low-background analysis of spectrally distinct fluorophores using a single long-wavelength laser. Extracts were prepared from immortalized rat raphe nuclei neurons, and were analyzed by CE-MPE. Native fluorescence was detected from reduced nicotinamide adenine dinucleotide (NADH) and its phosphorylated form (NADPH), flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), riboflavin, serotonin, and 5-hydroxytryptophan (5HTrp). Quantitation of exogenous serotonin (taken up by cells) and endogenous NADH and 5HTrp was possible using internal standards or standard addition. This system should be useful to study monamine oxidase inhibitors (MAOIs) and selective serotonin reuptake inhibitors (SSRIs).

Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets

Microbial production strains are currently improved using a combination of random and targeted approaches. In the case of a targeted approach, potential bottlenecks, feed-back inhibition, and side-routes are removed, and other processes of interest are targeted by overexpressing or knocking-out the gene(s) of interest. To date, the selection of these targets has been based at its best on expert knowledge, but to a large extent also on 'educated guesses' and 'gut feeling'. Therefore, time and thus money is wasted on targets that later prove to be irrelevant or only result in a very minor improvement. Moreover, in current approaches, biological processes that are not known to be involved in the formation of a specific product are overlooked and it is impossible to rank the relative importance of the different targets postulated. Metabolomics, a technology that involves the non-targeted, holistic analysis of the changes in the complete set of metabolites in the cell in response to environmental or cellular changes, in combination with multivariate data analysis (MVDA) tools like principal component discriminant analysis and partial least squares, allow the replacement of current empirical approaches by a scientific approach towards the selection and ranking of targets. In this review, we describe the technological challenges in setting up the novel metabolomics technology and the principle of MVDA algorithms in analyzing biomolecular data sets. In addition to strain improvement, the combined metabolomics and MVDA approach can also be applied to growth medium optimization, predicting the effect of quality differences of different batches of complex media on productivity, the identification of bioactives in complex mixtures, the characterization of mutant strains, the exploration of the production potential of strains, the assignment of functions to orphan genes, the identification of metabolite-dependent regulatory interactions, and many more microbiological issues.

On-line sample concentration techniques in capillary electrophoresis: velocity gradient techniques and sample concentration techniques for biomolecules

Methods with a high sensitivity and high separation efficiency are goals in analytical separation techniques. On-line sample concentration techniques in capillary electrophoresis (CE) separations have rapidly grown in popularity over the past few years because they achieve this goal. This review describes the methodology and theory associated with a number of different techniques, including electrokinetic and chromatographic methods. For small molecules, several on-line concentration methods based on velocity gradient techniques are described, in which the electrophoretic velocities of the analyte molecules are manipulated by field amplification, sweeping, and isotachophoretic migration, resulting in the on-line concentration of the analyte zones. In addition, the on-line concentration methods for macromolecules are described, since the techniques used for macromolecules (DNAs and proteins), are different from those for small molecules, with respect to either mechanism or methodology. Recent studies relating to this topic are also discussed, including electrophoretic and chromatographic techniques on capillary or microchip.

Phenolic extraction of DNA from mammalian tissues and conversion to deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides

Towards a goal of detecting scaled-up DNA adducts as altered deoxynucleotides by mass spectrometry, we have set up a practical and general method for isolating DNA-derived deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides starting with a 1 g sample of mammalian tissue. The method is practical because costs have been minimized, and it is general because it can be applied to a more difficult sample such as mouse skin or non-fresh calf liver. The procedure, consisting of a series of steps that were largely gleaned and tuned from prior literature, proceeds as follows: (1) homogenize the tissue in sodium dodecyl sulfate; (2) digest with ribonuclease A, ribonuclease TI, alpha-amylase and proteinase K; (3) partition between water and phenol; (4) precipitate the DNA with ethanol followed by redissolving and dialysis; and (5) digest with nuclease P1 and phosphodiesterase I followed by ultrafiltration and boric acid gel chromatography. The yellow to brown color of DNA from difficult tissues only persisted up to the ultrafiltration step. Apparently this DNA was contaminated with iron-containing proteins. Residual ribonucleotides were not observable (<0.1%) by HPLC in the final sample. Without boric acid gel chromatography, residual contamination by ribonucleotides was about 1% even when the DNA was purified before digestion by phenol partitioning followed by use of a Genomic Tip kit from Qiagen.

Sensitivity improvement on detection of Coptidis alkaloids by sweeping in capillary electrophoresis

A simple and rapid sweeping method for the online improvement of detection sensitivity of the main alkaloids of Coptidis Rhizoma has been developed in this work. Optimum separation conditions were found as follows: electrophoretic running solution comprising 100 mM phosphoric acid, 15 mM sodium dodecyl sulfate (SDS) and 10% (v/v) tetrahydrofurane with pH 1.82; running voltage of -25 kV; sample matrix composed of 50 mM phosphoric acid and sample injection at 1000 mbar for 60 s (sample injection volume ca. 2.75 microl). With this sweeping method, the concentration limits of detection of berberine, coptisine and palmatine were found to be 2.5 ppb (ng/ml), which was about 500 times lower than those from conventional sample injections. Baseline separation was achieved for the main alkaloids within 15 min. After validation, the developed method was applied to determine the quantity of berberine, coptisine and palmatine in a Coptidis Rhizoma sample. The method should be able to be used in identification and quantitative evaluation of the crude drugs requiring only a minor amount of sample.