In Vitro Assessment of Prebiotic Activity.

Bifidogenic effect is a main target for the assessment of prebiotic activity. pH-controlled batch processes of bifidobacteria and fecal microbiota are herein presented. Growth of bifidobacteria, carbohydrate breakdown and consumption, organic acid production, and activity of specific glycosyl hydrolases involved in the hydrolysis of di-, oligo-, or polysaccharides are exploited to study and compare substrate preference of bifidobacteria for candidate prebiotics.

Rapid Shotgun Phosphoproteomics Analysis.

In this chapter, we describe a rapid workflow for the shotgun global phosphoproteomics analysis. The strategy is based on the use of accelerated in-solution trypsin digestion under an ultrasonic field by high-intensity focused ultrasound (HIFU) coupled to titanium dioxide (TiO2) selective phosphopeptide enrichment, fractionation by strong cation exchange chromatography (SCX), and analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a high-resolution mass spectrometer (LTQ-Orbitrap XL). The strategy was optimized for the global phosphoproteome analysis of Jurkat T-cells. Using this accelerated workflow, HIFU-TiO2-SCX-LC-MS/MS, 15,367 phosphorylation sites from 13,029 different phosphopeptides belonging to 3,163 different phosphoproteins can be efficiently identified in less than 15 h.

Development and assessment of GC/MS and HPAEC/PAD methodologies for the quantification of α-galacto-oligosaccharides (GOS) in dry beans (Phaseolus vulgaris).

The quantification of α-Galacto-oligosaccharides (GOS) in beans has been increasingly approached through different methodologies. However, reported GOS contents revealed up to 8-times disparity, which cannot be only attributed to the bean cultivar and underlines the need of using validated analytical methodologies. This study aimed to optimize and validate the extraction of the most abundant GOS found in beans, namely raffinose, stachyose and verbascose, and comparatively assess their determination by High-Performance Anion Exchange Chromatography/Pulsed Amperometric Detector (HPAEC/PAD) and Gas Chromatography/Mass Spectrometry (GC/MS). Hot sonication followed by shaking with 70% ethanol resulted in excellent GOS extraction efficiencies (92.54-107.94%). GC/MS determination was more reliable than HPAEC/PAD, with limits of quantification of 4.48-224.31 mg/kg and intra/inter-day repeatabilities <10%. The analysis of six bean varieties proved the feasibility of the GC/MS methodology, displaying total GOS contents from 1453.07 ±â€¯169.31 to 2814.34 ±â€¯95.28 mg/100 g. Stachyose was significantly (p < 0.05) the main GOS in all samples.

Cross-scale quality assessment of a mechanistic cation exchange chromatography model.

Cation exchange chromatography (CEX) is an essential part of most monoclonal antibody (mAb) purification platforms. Process characterization and root cause investigation of chromatographic unit operations are performed using scale down models (SDM). SDM chromatography columns typically have the identical bed height as the respective manufacturing-scale, but a significantly reduced inner diameter. While SDMs enable process development demanding less material and time, their comparability to manufacturing-scale can be affected by variability in feed composition, mobile phase and resin properties, or dispersion effects depending on the chromatography system at hand. Mechanistic models can help to close gaps between scales and reduce experimental efforts compared to experimental SDM applications. In this study, a multicomponent steric mass-action (SMA) adsorption model was applied to the scale-up of a CEX polishing step. Based on chromatograms and elution pool data ranging from laboratory- to manufacturing-scale, the proposed modeling workflow enabled early identification of differences between scales, for example, system dispersion effects or ionic capacity variability. A multistage model qualification approach was introduced to measure the model quality and to understand the model's limitations across scales. The experimental SDM and the in silico model were qualified against large-scale data using the identical state of the art equivalence testing procedure. The mechanistic chromatography model avoided limitations of the SDM by capturing effects of bed height, loading density, feed composition, and mobile phase properties. The results demonstrate the applicability of mechanistic chromatography models as a possible alternative to conventional SDM approaches.

Maltoheptaoside hydrolysis with chromatographic detection and starch hydrolysis with reducing sugar analysis: Comparison of assays allows assessment of the roles of direct α-amylase inhibition and starch complexation.

The aim was to determine inhibition of human α-amylase activity by (poly)phenols using maltoheptaoside as substrate with direct chromatographic product quantification, compared to hydrolysis of amylose and amylopectin estimated using 3,5-dinitrosalicylic acid. Acarbose exhibited similar IC50 values (50% inhibition) with maltoheptaoside, amylopectin or amylose as substrates (2.37 ± 0.11, 3.71 ± 0.12 and 2.08 ± 0.01 µM respectively). Epigallocatechin gallate, quercetagetin and punicalagin were weaker inhibitors of hydrolysis of maltoheptaoside (<50% inhibition) than amylose (IC50: epigallocatechin gallate = 20.41 ± 0.25 µM, quercetagetin = 30.15 ± 2.05 µM) or amylopectin. Interference using 3,5-dinitrosalicylic acid was in the order punicalagin > epigallocatechin gallate > quercetagetin, with minimal interference using maltoheptaoside as substrate. The main inhibition mechanism of epigallocatechin gallate and punicalagin was through complexation with starch, especially amylose, whereas only quercetagetin additionally binds to the α-amylase active site. Interference is minimised using maltoheptaoside as substrate with product detection by chromatography, potentially allowing assessment of direct enzyme inhibition by almost any compound.

Quality assessment of supercoiled minicircle DNA by cadaverine-modified analytical chromatographic monolith.

Minicircle DNA (mcDNA) is the ultimate non-viral DNA vector, presenting higher biosafety and therapeutic effect than conventional plasmid DNA (pDNA). However, given the similarity between mcDNA and its precursor, the parental plasmid (PP), analytical methodologies established for pDNA are unable to distinguish mcDNA from PP. Thus, a new need emerged for the implementation of suitable, rapid and non-expensive analytical methodologies for the characterization of mcDNA samples. Recently, our research group was able to develop a purification strategy for the isolation of supercoiled (sc) mcDNA resorting to cadaverine-modified monolith. Considering the promising results obtained with this strategy, a cadaverine-modified analytical monolith was prepared and explored for mcDNA quantification. Thus, a strategy of three-step increasing NaCl gradient was considered to first elute RNA/protein content, then isolate sc mcDNA and finally eliminate PP and other impurities still bounded to the matrix. A calibration curve was constructed with different sc mcDNA standards within a range of 1-25 µg/mL. Linearity, accuracy, precision and selectivity of this method were validated according to the international guidelines and the limit of detection and the lower limit of quantification were determined as 1 µg/mL. For the first time, to the best of our knowledge, an analytical method for mcDNA quantification is described. Besides ensuring the safety of mcDNA application by assessing the product purity, such methodology can be used in the future to control industrial mcDNA production and purification, perhaps aiding in the establishment of optimized and less expensive biotechnological operations.

Structure-Function Assessment and High-Throughput Quantification of Site-Specific Aspartate Isomerization in Monoclonal Antibody Using a Novel Analytical Tool Kit.

Isomerization of surface-exposed aspartic acid (Asp) in the complementarity-determining regions of therapeutic proteins could potentially impact their target binding affinity because of the sensitive location, and often requires complex analytical tactics to understand its effect on structure-function and stability. Inaccurate quantitation of Asp-isomerized variants, especially the succinimide intermediate, presents major challenge in understanding Asp degradation kinetics, its stability, and consequently establishing a robust control strategy. As a practical solution to this problem, a comprehensive analytical tool kit has been developed, which provides a solution to fully characterize and accurately quantify the Asp-related product variants. The toolkit offers a combination of 2 steps, an ion-exchange chromatography method to separate and enrich the isomerized variants in the folded structure for structure-function evaluation and a novel focused peptide mapping method to quantify the individual complementarity-determining region isomerization components including the unmodified Asp, succinimide, and isoaspartate. This novel procedure allowed an accurate quantification of each Asp-related variant and a comprehensive assessment of the functional impact of Asp isomerization, which ultimately helped to establish an appropriate control strategy for this critical quality attribute.

CRDSAT Generated by pCARGHO: A New Efficient Lectin-Based Affinity Tag Method for Safe, Simple, and Low-Cost Protein Purification.

Purification of recombinant proteins remains a bottleneck for downstream processing. The authors engineered a new galectin 3 truncated form (CRDSAT ), functionally and structurally characterized, with preserved solubility and lectinic activity. Taking advantage of these properties, the authors designed an expression vector (pCARGHO), suitable for CRDSAT -tagged protein expression in prokaryotes. CRDSAT binds to lactose-Sepharose with a high specificity and facilitates solubilization of fusion proteins. This tag is structurally stable and can be easily removed from fusion proteins using TEV protease. Furthermore, due to their basic isoelectric point (pI), CRDSAT , and TEV are efficiently eliminated using cationic exchange chromatography. When pI of the protein of interest (POI) and CRDSAT are close, other chromatographic methods are successfully tested. Using CRDSAT tag, the authors purified several proteins from prokaryote and eukaryote origin and demonstrated as examples, the preservation of both Escherichia coli Thioredoxin 1 and human CDC25Bcd activities. Overall, yields of proteins obtained after tag removal are about 5-50 mg per litre of bacterial culture. Our purification method displays various advantages described herein that may greatly interest academic laboratories, biotechnology, and pharmaceutical companies.

Fast automated online xylanase activity assay using HPAEC-PAD.

In contrast to biochemical reactions, which are often carried out under automatic control and maintained overnight, the automation of chemical analysis is usually neglected. Samples are either analyzed in a rudimentary fashion using in situ techniques, or aliquots are withdrawn and stored to facilitate more precise offline measurements, which can result in sampling and storage errors. Therefore, in this study, we implemented automated reaction control, sampling, and analysis. As an example, the activities of xylanases on xylotetraose and soluble xylan were examined using high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD). The reaction was performed in HPLC vials inside a temperature-controlled Dionex™ AS-AP autosampler. It was started automatically when the autosampler pipetted substrate and enzyme solution into the reaction vial. Afterwards, samples from the reaction vial were injected repeatedly for 60 min onto a CarboPac™ PA100 column for analysis. Due to the rapidity of the reaction, the analytical method and the gradient elution of 200 mM sodium hydroxide solution and 100 mM sodium hydroxide with 500 mM sodium acetate were adapted to allow for an overall separation time of 13 min and a detection limit of 0.35-1.83 mg/L (depending on the xylooligomer). This analytical method was applied to measure the soluble short-chain products (xylose, xylobiose, xylotriose, xylotetraose, xylopentaose, and longer xylooligomers) that arise during enzymatic hydrolysis. Based on that, the activities of three endoxylanases (EX) were determined as 294 U/mg for EX from Aspergillus niger, 1.69 U/mg for EX from Bacillus stearothermophilus, and 0.36 U/mg for EX from Bacillus subtilis. Graphical abstract Xylanase activity assay automation.

Assessment of plasma amino acid profile in autism using cation-exchange chromatography with postcolumn derivatization by ninhydrin.

BACKGROUND/AIM: Autism is a heterogeneous neurodevelopmental disorder. This study aimed to assess the clinical significance of amino acid profile assay in autism using cation-exchange chromatography with ninhydrin postcolumn derivatization. MATERIALS AND METHODS: This study included 42 autistic children and 26 apparently healthy children. All participants were subjected to the assay of plasma amino acids (essential, nonessential, and nonstandard) using cation-exchange chromatography with postcolumn derivatization by ninhydrin. RESULTS: The levels of most of the essential amino acids were significantly lower in autistic children than controls. As regards nonessential amino acids, significantly lower levels for plasma cysteine, tyrosine, and serine and significantly higher levels for plasma glutamic acid were recorded in autistic children than controls. Finally, the autistic group demonstrated significantly lower levels of α-aminoadipic acid, carnosine, and ß-alanine and significantly higher levels of hydroxyproline, phosphoserine, ß-amino-isobutyric acid, and ammonia as compared to controls. CONCLUSION: The study revealed that autistic children exhibit distinct alterations in the plasma levels of some amino acids, which can in turn participate in the disease etiology and can be applied as a diagnostic tool for early detection of autism.

One-step chromatographic procedure for purification of B-phycoerythrin from Porphyridium cruentum.

B-phycoerythrin (B-PE) was separated and purified from microalga Porphyridium cruentum using one-step chromatographic method. Phycobiliproteins in P. cruentum was extracted by osmotic shock and initially purified by ultrafiltration. Further purification was carried out with a SOURCE 15Q exchange column and analytical grade B-PE was obtained with a purity ratio (A545/A280) of 5.1 and a yield of 68.5%. It showed a double absorption peaks at 545 nm and 565 nm and a shoulder peak at 498 nm, and displayed a fluorescence emission maximum at 580 nm. The analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed a bulky band between 18 and 20 kDa which could be assigned to subunits α and ß and a low intensity band of 27 kDa assigned to γ subunit. Our protocol provides attractive alternative to consider for the purification procedure to obtain analytical grade B-PE at commercial level.

Rapid measurement of perchlorate in polar ice cores down to sub-ng L(-1) levels without pre-concentration.

An ion chromatography-electrospray ionization-tandem mass spectrometry (IC-ESI-MS/MS) method has been developed for rapid and accurate measurement of perchlorate in polar snow and ice core samples in which perchlorate concentrations are expected to be as low as 0.1 ng L(-1). Separation of perchlorate from major inorganic species in snow is achieved with an ion chromatography system interfaced to an AB SCIEX triple quadrupole mass spectrometer operating in multiple reaction monitoring mode. Under optimized conditions, the limit of detection and lower limit of quantification without pre-concentration have been determined to be 0.1 and 0.3 ng L(-1), respectively, with a linear dynamic range of 0.3-10.0 ng L(-1) in routine measurement. These represent improvements over previously reported methods using similar analytical techniques. The improved method allows fast, accurate, and reproducible perchlorate quantification down to the sub-ng L(-1) level and will facilitate perchlorate measurement in the study of natural perchlorate production with polar ice cores in which perchlorate concentrations are anticipated to vary in the low and sub-ng L(-1) range. Initial measurements of perchlorate in ice core samples from central Greenland show that typical perchlorate concentrations in snow dated prior to the Industrial Revolution are about 0.8 ng L(-1), while perchlorate concentrations are significantly higher in recent (post-1980) snow, suggesting that anthropogenic sources are a significant contributor to perchlorate in the current environment.

Implementation of a high-throughput ion chromatographic assay to assess glass degradation in drug product formulations.

UNLABELLED: The primary container for parenterals is usually composed of glass. Given the recent industry-wide spike in glass-related problems, assays capable of detecting glass degradation before glass-related particles are visible in solution have practical significance. A rapid, high-throughput ion chromatography method coupled with molybdate reaction is described here for detection and quantitation of silicic acid (soluble form of silica) in complex samples. The method involves ion exchange separation of the silicate anion at high pH followed by a post-column derivatization step with sodium molybdate reagent. The resulting molybdo-silicate complex is detected with high sensitivity in the visible wavelength range at 410 nm and correlates to the level of soluble silica in solution. This assay is high-throughput and amenable for implementation during the early phase of product development. The assay provides a direct measurement to assess potential incompatibility between the formulation and its glass container. The Si levels measured by this method showed a direct correlation to the vial surface morphology changes as monitored by differential interference contrast microscopy. LAY ABSTRACT: Recently, the pharmaceutical industry has been faced with glass quality challenges that have resulted in many products being recalled from the market. Monitoring levels of soluble silica in solution is critical because silica is the primary component of glass containers used in the pharmaceutical industry. Given this recent industry-wide increase in glass-related problems, assays capable of detecting glass degradation before glass-related particles are visible in solution have practical significance. A rapid assay to detect the soluble form of silica is presented here. The method presented will enable earlier detection of a formulation and container incompatibility instead of waiting until glass-related particles are visible in solution.

A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography.

In downstream processing, the underlying adsorption mechanism of biomolecules to adsorbent material are still subject of extensive research. One approach to more mechanistic understanding is simulating this adsorption process and hereby the possibility to identify the parameters with strongest impact. So far this method was applied with all-atom molecular dynamics simulations of two model proteins on one cation exchanger. In this work we developed a molecular dynamics tool to simulate protein-adsorber interaction for various proteins on an anion exchanger and ran gradient elution experiments to relate the simulation results to experimental data. We were able to show that simulation results yield similar results as experimental data regarding retention behavior as well as binding orientation. We could identify arginines in case of cation exchangers and aspartic acids in case of anion exchangers as major contributors to binding.

Assessment of capillary anion exchange ion chromatography tandem mass spectrometry for the quantitative profiling of the phosphometabolome and organic acids in biological extracts.

Metabolic profiling has become an important tool in biological research, and the chromatographic separation of metabolites coupled with mass spectrometric detection is the most frequently used approach for such studies. The establishment of robust chromatographic methods for comprehensive coverage of the anionic metabolite pool is especially challenging. In this study, the development of a capillary ion exchange chromatography (capIC) - negative ESI tandem mass spectrometry (MS/MS) workflow for the quantitative profiling of the phosphometabolome (e.g., sugar phosphates and nucleotides) is presented. The chromatographic separation and MS/MS conditions were optimized, and the precision of repetitive injections and accuracy in terms of error percentage to true concentration were assessed. The precision is excellent for a capillary flow system with an average CV% of 8.5% for a 50-fmol standard injection and in the lower 2.4-4.4% range for higher concentrations (500-7,500 fmol). The limit of detection (LOD) ranges from 1 to 100 nM (5-500 fmol injected on column), and the limit of quantitation (LOQ) ranges from 1 to 500 nM (5-2,500 fmol injected on column). A fast gradient method with the injection of 50% methanol in water between analytical samples is needed to eliminate carry-over and ensure optimal re-equilibration of the column. Finally, the quantitative applicability of the system was tested on real biological matrices using the constant-volume standard addition method (SAM). Extracts of the human kidney Hek293 cell line were spiked with increasing concentrations of standards to determine the concentration of each metabolite in the sample. Forty-four metabolites were detected with an average uncertainty of 4.1%. Thus, the capIC-MS/MS method exhibits excellent selectivity, sensitivity and precision for the quantitative profiling of the phosphometabolome.

Application of ion chromatography in clinical studies and pharmaceutical industry.

Ion chromatography is a well-established regulatory method for analyzing anions and cations in environmental, food and many other samples. It offers an enormous range of possibilities for selecting stationary and mobile phases. Additionally, it usually helps to solve various separation problems, particularly when it is combined with different detection techniques. Ion chromatography can also be used to determine many ions and substances in clinical and pharmaceutical samples. It provides: availability of high capacity stationary phases and sensitive detectors; simple sample preparation; avoidance of hazardous chemicals; decreased sample volumes; flexible reaction options on a changing sample matrix to be analyzed; or the option to operate a fully-automated system. This paper provides a short review of the ion chromatography applications for determining different inorganic and organic substances in clinical and pharmaceutical samples.

Determination of total iodine in serum and urine samples by ion chromatography with pulsed amperometric detection - studies on analyte loss, optimization of sample preparation procedures, and validation of analytical method.

A fast, accurate and precise ion chromatography method with pulsed amperometric detection was applied to evaluate a variety of parameters affecting the determination of total iodine in serum and urine of 81 subjects, including 56 obese and 25 healthy Polish children. The sample pretreatment methods were carried out in a closed system and with the assistance of microwaves. Both alkaline and acidic digestion procedures were developed and optimized to find the simplest combination of reagents and the appropriate parameters for digestion that would allow for the fastest, least time consuming and most cost-effective way of analysis. A good correlation between the certified and the measured concentrations was achieved. The best recoveries (96.8% for urine and 98.8% for serum samples) were achieved using 1ml of 25% tetramethylammonium hydroxide solution within 6min for 0.1ml of serum/urine samples. Using 0.5ml of 65% nitric acid solution the best recovery (95.3%) was obtained when 7min of effective digestion time was used. Freeze-thaw stability and long-term stability were checked. After 24 weeks 14.7% loss of iodine in urine, and 10.9% in serum samples occurred. For urine samples, better correlation (R(2)=0.9891) of various sample preparation procedures (alkaline digestion and application of OnGuard RP cartidges) was obtained. Significantly lower iodide content was found in samples taken from obese children. Serum iodine content in obese children was markedly variable in comparison with the healthy group, whereas the difference was less evident when urine samples were analyzed. The mean content in serum was 59.12±8.86µg/L, and in urine 98.26±25.93 for obese children when samples were prepared by the use of optimized alkaline digestion reinforced by microwaves. In healthy children the mean content in serum was 82.58±6.01µg/L, and in urine 145.76±31.44µg/L.

Preparation and quality assessment of high-purity ginseng total saponins by ion exchange resin combined with macroporous adsorption resin separation.

AIM: To prepare high-purity ginseng total saponins from a water decoction of Chinese ginseng root. METHOD: Total saponins were efficiently purified by dynamic anion-cation exchange following the removal of hydrophilic impurities by macroporous resin D101. For quality control, ultrahigh-performance liquid chromatography with a charged aerosol detector (CAD) was applied to quantify marker components. The total saponin content was estimated by a colorimetric method using a vanillin-vitriol system and CAD response. RESULTS: D201, which consisted of a cross-linked polystyrene matrix and -N(+)(CH3)3 functional groups, was the best of the four anion exchange resins tested. However, no significant difference in cation exchange ability was observed between D001 (strong acid) and D113 (weak acid), although they have different functional groups and matrices. After purification in combination with D101, D201, and D113, the estimated contents of total saponins were 107% and 90% according to the colorimetric method and CAD response, respectively. The total amount of representative ginsenosides Re, Rd, Rg1, and compound K was approximately 22% based on ultrahigh-performance liquid chromatography-CAD quantitative analysis. CONCLUSION: These findings suggest that an ion exchange resin, combined with macroporous adsorption resin separation, is a promising and feasible purification procedure for neutral natural polar components.

Evaluation of high-capacity cation exchange chromatography for direct capture of monoclonal antibodies from high-titer cell culture processes.

Advances in molecular biology and cell culture technology have led to monoclonal antibody titers in excess of 10 g/L. Such an increase can pose concern to traditional antibody purification processes due to limitations in column hardware and binding capacity of Protein A resins. Recent development of high capacity cation exchangers can make cation exchange chromatography (CEX) a promising and economic alternative to Protein A capture. This work investigates the feasibility of using CEX for direct capture of monoclonal antibodies from high titer cell culture fluids. Two resin candidates were selected from seven newer generation cation exchangers for their higher binding capacity and selectivity. Two monoclonal antibodies with widely differing pI values were used to evaluate the capability of CEX as a platform capture step. Screening of loading pH and conductivity showed both resins to be capable of directly capturing both antibodies from undiluted cell culture fluid. At appropriate acidic pH range, product loading of over 65 g/L resin was achieved for both antibodies. A systematic design of experiment (DOE) approach was used to optimize the elution conditions for the CEX step. Elution pH showed the most significant impact on clearance of host cell proteins (HCPs). Under optimal conditions, HCP reduction factors in the range of 9-44 were achieved on the CEX step based on the pI of the antibody. Apart from comparing CEX directly to Protein A as the capture method, material from either modality was also processed through the subsequent polishing steps to compare product quality at the drug substance level. Process performance and product quality was found to be acceptable using the non-affinity based process scheme. The results shown here present a cheaper and higher capacity generic capture method for high-titer antibody processes.

Developing a strong anion exchange/RP (SAX/RP) 2D LC system for high-abundance proteins depletion in human plasma.

Human plasma is dominated by high-abundance proteins which severely impede the detection of low-abundance proteins. Unfortunately, now there is no efficient method for large-scale depletion of high-abundance proteins in human plasma. In this study, we developed a new strategy, strong anion exchange (SAX)/RP 2D LC system, which has potential for large-scale depletion of high-abundance proteins in human plasma. Separation gradients of the system were optimized to ensure an extensive separation of plasma proteins. Plasma was fractionated into 67 fractions by SAX. All these fractions were subjected a thorough separation by the 2D RPLC and 66 peaks with high UV absorption (>20 mAU) at 215 nm were collected. Proteins in these peaks were identified by LC-MS/MS analysis. Results showed that 83 proteins could be identified in these peaks, 68 among them were reported to be high- or middle-abundance proteins in plasma. All these proteins had definite retention times and were mapped in the 2D SAX-RP system, which resulted in accurate depletion of high-abundance proteins with ease. Our studies provide a convenient and effective method for large-scale depletion of high-abundance proteins and in-depth research in human plasma proteomics.