Capillary electrophoresis at the omics level: Towards systems biology

Analytical Strategies to Investigate Molecular Signaling, Proteomics, Extraction and Quantification of Withanolides - A Comprehensive Review

Withanolides are the class of steroidal molecules getting greater emphasis in recent years. Quality control throughout the manufacturing and storage period is often one of the key problems that have restricted their broad use in India's indigenous and Ayurvedic medical systems for thousands of years. Because of their diverse clinical potential, withanolides have received a great deal of scientific attention. Analytical techniques are being devised for the automated isolation, identification, and estimation of every single protein within the cell as well as in herbal extracts of withanolides, due to which now researchers are interested in determining the effects of metabolism as well as various stimuli on protein expression, which made the study easier. This study discusses the potential use of hyphenated analytical methods that are reliable in understanding the molecular signaling features, proteome evaluation and characterization of withanolides, in addition to examining existing methodological limitations. The choice of analytical techniques for the withanolides analysis, however, relies on the nature of the sample matrix, the aim of the analysis, and the sensitivity of the technique.

Use of Foodomics for Control of Food Processing and Assessing of Food Safety

Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.

Capillary Electrophoresis in Metabolomics

Metabolomics is an analytical toolbox to describe (all) low-molecular-weight compounds in a biological system, as cells, tissues, urine, and feces, as well as in serum and plasma. To analyze such complex biological samples, high requirements on the analytical technique are needed due to the high variation in compound physico-chemistry (cholesterol derivatives, amino acids, fatty acids as SCFA, MCFA, or LCFA, or pathway-related metabolites belonging to each individual organism) and concentration dynamic range. All main separation techniques (LC-MS, GC-MS) are applied in routine to metabolomics hyphenated or not to mass spectrometry, and capillary electrophoresis is a powerful high-resolving technique but still underused in this field of complex samples. Metabolomics can be performed in the non-targeted way to gain an overview on metabolite profiles in biological samples. Targeted metabolomics is applied to analyze quantitatively pre-selected metabolites. This chapter reviews the use of capillary electrophoresis in the field of metabolomics and exemplifies solutions in metabolite profiling and analysis in urine and plasma.

Dilution of protein-surfactant complexes: a fluorescence study

Dilution of protein-surfactant complexes is an integrated step in microfluidic protein sizing, where the contribution of free micelles to the overall fluorescence is reduced by dilution. This process can be further improved by establishing an optimum surfactant concentration and quantifying the amount of protein based on the fluorescence intensity. To this end, we study the interaction of proteins with anionic sodium dodecyl sulfate (SDS) and cationic hexadecyl trimethyl ammonium bromide (CTAB) using a hydrophobic fluorescent dye (sypro orange). We analyze these interactions fluourometrically with bovine serum albumin, carbonic anhydrase, and beta-galactosidase as model proteins. The fluorescent signature of protein-surfactant complexes at various dilution points shows three distinct regions, surfactant dominant, breakdown, and protein dominant region. Based on the dilution behavior of protein-surfactant complexes, we propose a fluorescence model to explain the contribution of free and bound micelles to the overall fluorescence. Our results show that protein peak is observed at 3 mM SDS as the optimum dilution concentration. Furthermore, we study the effect of protein concentration on fluorescence intensity. In a single protein model with a constant dye quantum yield, the peak height increases with protein concentration. Finally, addition of CTAB to the protein-SDS complex at mole fractions above 0.1 shifts the protein peak from 3 mM to 4 mM SDS. The knowledge of protein-surfactant interactions obtained from these studies provides significant insights for novel detection and quantification techniques in microfluidics.

MS-based analytical methodologies to characterize genetically modified crops

The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.

Metabolic Profiling of Human Blood by High Resolution Ion Mobility Mass Spectrometry (IM-MS)

A high resolution ion mobility time-of-flight mass spectrometer with electrospray ionization source (ESI-IM-MS) was evaluated as an analytical method for rapid analysis of complex biological samples such as human blood metabolome was investigated. The hybrid instrument (IM-MS) provided an average ion mobility resolving power of ~90 and a mass resolution of ~1500 (at m/z 100). A few µL of whole blood was extracted with methanol, centrifuged and infused into the IM-MS via an electrospray ionization source. Upon IM-MS profiling of the human blood metabolome approximately 1,100 metabolite ions were detected and 300 isomeric metabolites separated in short analyses time (30 minutes). Estimated concentration of the metabolites ranged from the low micromolar to the low nanomolar level. Various classes of metabolites (amino acids, organic acids, fatty acids, carbohydrates, purines and pyrimidines etc) were found to form characteristic mobility-mass correlation curves (MMCC) that aided in metabolite identification. Peaks corresponding to various sterol derivatives, estrogen derivatives, phosphocholines, prostaglandins, and cholesterol derivatives detected in the blood extract were found to occupy characteristic two dimensional IM-MS space. Low abundance metabolite peaks that can be lost in MS random noise were resolved from noise peaks by differentiation in mobility space. In addition, the peak capacity of MS increased six fold by coupling IMS prior to MS analysis.

Simple device for multiplexed electrophoretic separations using gradient elution moving boundary electrophoresis with channel current detection

A new microfluidic electrophoresis device and technique is described that is designed specifically for multiplexed, high-throughput separations. The device consists of an array of short (3 mm) capillaries connecting individual sample reservoirs to a common buffer reservoir. Each capillary in the array functions as both a separation channel and as a conductivity-based detection cell. The new technique is based upon the recently described gradient elution moving boundary electrophoresis (GEMBE) technique, which uses a combination of an electric field and buffer counterflow to achieve electrophoretic separations in short capillaries or microfluidic channels. A high voltage drives electrophoresis of the sample analytes through each separation channel. At the start of a separation, the bulk counterflow of buffer through the channel is high, and none of the analytes of interest can enter the channel. The counterflow is then gradually reduced until each analyte, in turn, is able to enter the channel where it is detected as a moving boundary or step. With very short capillaries, only one step at a time is present in each capillary, and the electric current through the channels can then be used as the detector signal, without any extra detector hardware. The current vs time signal for each channel is then smoothed and differentiated to produce a set of simultaneous electropherograms. Because there is no light source or other added hardware required for detection, the system is simple and can be easily and inexpensively scaled up to perform large numbers of simultaneous analyses. As a first demonstration, a 16-channel array device is used for high-throughput, time-series measurements of enzyme activity and inhibition.

Review: Microfluidic applications in metabolomics and metabolic profiling

Metabolomics is an emerging area of research focused on measuring small molecules in biological samples. There are a number of different types of metabolomics, ranging from global profiling of all metabolites in a single sample to measurement of a selected group of analytes. Microfluidics and related technologies have been used in this research area with good success. The aim of this review article is to summarize the use of microfluidics in metabolomics. Direct application of microfluidics to the determination of small molecules is covered first. Next, important sample preparation methods developed for microfluidics and applicable to metabolomics are covered. Finally, a summary of metabolomic work as it relates to analysis of cellular events using microfluidics is covered.

Advances in separation science applied to metabonomics

Metabonomics focuses on metabolite profile changes in diverse living systems caused by a biological perturbation. These metabolite signatures can be achieved with techniques such as gas chromatography, high-performance liquid chromatography (ultra-high-performance/pressure liquid chromatography and capHPLC), capillary electrophoresis, and capillary electrochromatography normally hyphenated with MS. In this review we present the latest developments of the abovementioned techniques applied in the field of metabonomics, with applications covering phytochemistry, toxicology and clinical research.

Development of a capillary electrophoresis-mass spectrometry method using polymer capillaries for metabolomic analysis of yeast

Metabolomics is an emerging field in analytical biochemistry, and the development of such a method for comprehensive and quantitative analysis of organic acids, carbohydrates, and nucleotides is a necessity in the era of functional genomics. When a concentrated yeast extract was analyzed by CE-MS using a successive multiple ionic-polymer layer (SMIL)-coated capillary, the adsorption of the contaminants on the capillary wall caused severe problems such as no elution, band-broadening, and asymmetric peaks. Therefore, an analytical method for the analysis of anionic metabolites in yeast was developed by pressure-assisted CE using an inert polymer capillary made from poly(ether etherketone) (PEEK) and PTFE. We preferred to use the PEEK over the PTFE capillary in CE-MS due to the easy-to-use PEEK capillary and its high durability. The separation of anionic metabolites was successfully achieved with ammonium hydrogencarbonate/formate buffer (pH 6.0) as the electrolyte solution. The use of 2-propanol washing after every electrophoresis run not only eliminated wall-adsorption phenomena, but allowed for good repeatability to be obtained for migration times in the metabolomic analysis.

Measurement of phosphorylated phospholamban levels in cardiomyocytes (HL-1) by immunoprecipitation

Phospholamban (PLN) is a key regulatory protein involved in cardiac calcium signaling through the pumping of cytoplasmic Ca2+ into the sarcoplasmic reticulum (SR). Recent systems-level studies have focused on integrating quantitative data (e.g. protein expression levels) for a better understanding of cardiac systems biology. In this view, we developed a capillary electrophoresis (CE) based immunoprecipitation method for the measurement of phospho-PLN (ser 16) in cardiomyocytes (HL-1 cell line). Dose-dependent isoproterenol (Iso) treated cells were analyzed using CE, and the phospho-PLN levels were quantified using specific polyclonal antibodies. The CE method employed was accurate, quick and easier compare to other techniques and the results are useful for the subsequent computational systems biology research.

Characterization of voltage degradation in dynamic field gradient focusing

Dynamic field gradient focusing (DFGF) is an equilibrium gradient method that utilizes an electric field gradient to simultaneously separate and concentrate charged analytes based on their individual electrophoretic mobilities. This work describes the use of a 2-D nonlinear, numerical simulation to examine the impact of voltage loss from the electrodes to the separation channel, termed voltage degradation, and distortions in the electric field on the performance of DFGF. One of the design parameters that has a large impact on the degree of voltage degradation is the placement of the electrodes in relation to the separation channel. The simulation shows that a distance of about 3 mm from the electrodes to the separation channel gives the electric field profile with least amount of voltage degradation. The simulation was also used to describe the elution of focused protein peaks. The simulation shows that elution under constant electric field gradient gives better performance than elution through shallowing of the electric field. Qualitative agreement between the numerical simulation and experimental results is shown. The simulation also illustrates that the presence of a defocusing region at the cathodic end of the separation channel causes peak dispersion during elution. The numerical model is then used to design a system that does not suffer from a defocusing region. Peaks eluted under this design experienced no band broadening in our simulations. Preliminary experimental results using the redesigned chamber are shown.

Capillary electrophoresis as a metabolomic tool in antioxidant therapy studies

The development of an approach by which two CE methods operating with opposite polarities and orthogonal capillary electrophoretic separation modes (method 1: normal polarity cyclodextrin modified MEKC (CD-MEKC) and method 2: reversed polarity CZE) for the sequential application to urinary samples from a type I diabetes metabolomics investigation is discussed. During method development, problematic MEKC profile drift issues arising from the high glucose content of the diabetic animal urine samples required some electrolyte modifications involving the use of hexafluoroisopropanol (HFIP) to circumvent the drift. Data derived from both methods were subsequently subjected to alignment, normalization and multi-dimensional scaling (MDS) procedures. In such a way, classification of samples derived from control and diabetic animals receiving a placebo from those receiving an antioxidant nutraceutical, was successfully demonstrated. Such a strategy is a cost effective and comprehensive metabolomics tool useful for describing UV absorbing metabolite disease-related changes in nutra/pharma-ceutical studies.

Quantification of rRNA in Escherichia coli using capillary gel electrophoresis with laser-induced fluorescence detection

Over the past 10 years, sophisticated powerful techniques have been developed for the quantification of messenger RNA (mRNA) and ribosomal RNA (rRNA), enabling researchers in science, industry, and molecular medicine to explore gene expression. These techniques require the (reverse) transcription of analyte RNA, hybridization with synthetic oligonucleotides, and other additional steps that make them costly, time-consuming, and quantitatively difficult to perform. The current work demonstrates how 16S and 23S rRNA can be quantified precisely using capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) directly after the extraction of total RNA without requiring further reactions or calibration. CGE-LIF normally is used for the qualitative examination of RNA preparations. Its quantitative performance could be improved significantly using MS2 bacteriophage RNA as an internal standard. The entire analytical procedure was validated for linearity, repeatability, reproducibility, and recovery. This validation also included total RNA extraction from bacterial cells, an aspect examined for the first time in absolute RNA quantification. Recovery is close to 100%, and the analytical precision was increased 10-fold (CV<3%), as compared with similar approaches. The demonstrated method is simple and opens up new possibilities for the absolute quantification of not only rRNA but also individual mRNAs.

Experimental design optimization of the capillary electrophoresis separation of leucine enkephalin and its immune complex

To optimize the capillary electrophoretic separation conditions for leucine enkephalin (LE) and the immune complex of the LE and anti-LE reaction, an analysis using a three-level, three-factorial Box-Behnken design was performed. Three separation parameters, buffer pH (X(1)), buffer concentration (X(2)), and applied voltage (X(3)), were chosen to observe the effect on separation responses. The responses were theoretical plate number, migration time of the LE peak, and resolution between the peaks. The optimum conditions and process validation were determined using statistical regression analysis and surface plot diagrams. The capillary electrophoresis optimum separation conditions were established to be 75 mM phosphate buffer at pH 7.00 with an applied separation voltage of 15 kV. By using the analysis technique, the prediction of responses was satisfactory and process verification yielded values within the +/-5% range of the predicted efficiency.

Quantitative analysis of sulfur-related metabolites during cadmium stress response in yeast by capillary electrophoresis–mass spectrometry

The objective of this research is to establish an evaluation system of metabolites by capillary electrophoresis-mass spectrometry (CE-MS) in response to chemical stress using the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C). A method previously reported by Soga et al. was modified and validated for the determination of sulfur-related metabolites, 23 cationic metabolites, in yeast extract. A mixture of 5 mM formic acid in 50% (v/v) 2-propanol was used for the sheath liquid to improve the detection sensitivity. Moreover, washing of CE capillary with 0.1M ammonia solution between successive runs enhanced the reproducibility. After analytical validation, the method was applied to the metabolomic analysis of yeast cells in response to cadmium (Cd) stress. Under Cd exposure, some interesting observations were obtained, particularly the depletion of glycine and the strong accumulation of L-gamma-glutamylcysteine in yeast cells.

Capillary electrophoresis of signaling molecules

The emerging field of quantitative systems biology uses high-throughput bioanalytical measurements to gain a deeper understanding of biological phenomena. With the advent of instrumentation platforms, capillary electrophoresis spans a very wide range of biological applications. This short article focuses on the exploitation of capillary electrophoresis for the systems-level analysis of cell signaling molecules.