Development and validation of indirect RP-HPLC method for enantiomeric purity determination of D-cycloserine drug substance

A new chiral purity method was developed for D-cycloserine (D-cys) by reverse phase HPLC and validated. Chiral derivatizing reagents, viz., o-phthalaldehyde and N-acetyl-L-cysteine were utilized in this method. The resultant diastereomers were resolved using Zorbax SB Phenyl HPLC column under isocratic elution. A mobile phase of 95:05 (v/v), 20mM Na(2)HPO(4) (pH 7), and acetonitrile, respectively, was used with the flow rate of 1.0 mL/min and UV detection at 335 nm. The method development with different chiral stationary phases and chiral derivatization reagents were also investigated. The stability of diastereomer derivative and influence of organic modifier and pH of the mobile phase were studied and optimized. The stability-indicating capability of the method was established by performing stress studies under acidic, basic, oxidation, light, humidity and thermal conditions. The detection and quantitation limit of L-cycloserine (L-cys) were 0.015 and 0.05% (w/w), respectively. A linear range from 0.05 to 0.30% (w/w) was obtained with the coefficient of determination (r(2)) 0.998. The recovery obtained for L-cys was between 92.9 and 100.2%. This method was applied successfully in pharmaceutical analysis to determine the content of L-cys in D-cys bulk drug.

Proteomic analysis of thylakoid membranes

Chlamydomonas is a model organism to study photosynthesis. Thylakoid membranes comprise several proteins belonging to photosystems I and II. In this chapter, we show the accurate proteomic measurements in thylakoid membranes. The chlorophyll-containing membrane protein complexes were precipitated using chloroform/methanol solution. These complexes were separated using two-dimensional gel electrophoresis, and the resolved spots were exercised from the gel matrix and digested with trypsin. These peptide fragments were separated by MALDI-TOF, and the isotopic masses were blasted to a MASCOT server to obtain the protein sequence. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF). The method discussed here would be a useful method for the separation and identification of thylakoid membrane proteins.

Residue content of carbaryl applied on greenhouse cucumbers and its reduction by duration of a pre-harvest interval and post-harvest household processing

BACKGROUND

Carbaryl is widely used to control various insect pests on greenhouse cucumbers in Iran. Therefore the control of residual levels of this insecticide is highly necessary. The effects of the household processing such as washing, peeling and refrigeration storage, at 4 °C for 2 days on the reduction of residue levels in the plant tissues were investigated in the different groups. Samples were collected at 1 h to 14 days after application and analysed to determine the content and dissipation rate of carbaryl. Analysis was carried out by the QuEChERS method using HPLC-UV.

RESULTS

Carbaryl residue in samples, which were collected post-application in different times showed a gradual and significant (P < 0.05) decrease. The half-life (t(1/2)) of carbaryl applied on cucumbers was 3.2 days. Carbaryl residues were detected in concentration ranges of 0.22-4.91 mg kg(-1). Also, the results indicated that the consumable safety time of carbaryl was found to be more than 14 days on cucumber.

CONCLUSION

Household processing, such as washing and peeling and refrigeration storage, was effective in reducing the residue levels. Also, peeling was the most effective way to reduce the carbaryl residues of the cucumber samples. Washing and refrigerated storage also decreased carbaryl residues.

Effect of saliva processing on bacterial DNA extraction

More than 700 bacterial species inhabit oral cavity of humans. Various oral diseases are related to changes in the structure of this complex community. Their pathogenesis can, thus, be better understood by study of oral microbial flora. As many bacteria are refractory to cultivation, molecular approaches based on PCR followed by downstream analysis are more suitable for community analysis than culture dependent methods. Effective DNA extraction from the sample matrix is a fundamental part of the pre-analytical phase but it can be influenced by processing of the starting material. The aim of this study was to analyze the effects of saliva processing on DNA extraction using several non-commercial isolation procedures. Bacterial chromosomal DNA was extracted from three different sample matrices: fresh saliva, diluted saliva and pelleted saliva using four different extraction methods: phenol chloroform protocol, benzyl-chloride protocol, extraction with Chelex-100 and extraction with Triton X. Extraction from different saliva samples and the use of different extraction methods significantly affected the effectiveness of DNA extraction. The most suitable material for bacterial DNA extraction for molecular analysis is a fresh saliva sample. The most effective methods for isolating salivary DNA are the benzyl-chloride protocol and Chelex-100 extraction. Our results have implications for studies concentrating on salivary microbiome and its role in the pathogenesis of oral diseases.

Fast and simple droplet sampling of sap from plant tissues and capillary microextraction of soluble saccharides for picogram-scale quantitative determination with GC-MS

Soluble saccharides are very important metabolites of the life cycle and synthesis of structural polysaccharide components (cellulose, hemicellulose, pectin, etc.) of cell walls. A new method for droplet sampling of saps from tissues of organisms and manipulation routines in capillaries for extraction, derivation, and partitioning were developed for picogram-scale quantitative determination with gas chromatography-mass spectrometry (GC-MS). Five to ten microliters of sap was sampled with a glass capillary containing ribitol (internal standard). Subsequently, the analytes were acetylated with acetic anhydride and catalyzed by 1-methylimidazole. Finally, the soluble saccharides were qualitatively detected with GC-MS SIM (selective ion monitoring) mode. The linear ranges of the method were up to 1×10(-6) mol/L and the theoretically lowest limits of detection (LOD, s/n≥3) were up to 1×10(-9) mol/L. The method is suitable and applicable to analysis of soluble monosaccharides in fresh tissues and other aqueous samples in wide fields of agriculture, food science, biological sciences, and even medical studies.

Liquid crystalline elastomers as actuators and sensors

This review collects recent developments in the field of liquid crystalline elastomers (LCEs) with an emphasis on their use for actuator and sensor applications. Several synthetic pathways leading to crosslinked liquid crystalline polymers are discussed and how these materials can be oriented into liquid crystalline monodomains are described. By comparing the actuating properties of different systems, general structure-property relationships for LCEs are obtained. In the final section, how these materials can be turned into usable devices using different interdisciplinary techniques are described.

High-throughput analysis of total plasma fatty acid composition with direct in situ transesterification

Background

Plasma fatty acid (FA) composition reflects dietary intake and endogenous turnover and is associated with health outcomes on a short and long term basis. The total plasma FA pool represents the composition of all FA containing lipid fractions. We developed a simplified and affordable high-throughput method for the analysis of total plasma FA composition, suitable for large studies.

Methodology/Principal Findings

The total lipid FA from 100 µl plasma is transferred in situ into methyl esters, avoiding initial extraction and drying steps. The fatty acid methyl esters are extracted once and analyzed by gas chromatography. For the new direct in situ transesterification method optimal, reaction parameters were determined. Intra-assay analysis (n = 8) revealed coefficients of variation below 4% for FA contributing more than 1% to total FA.

Conclusions/Significance

The results show good agreement with FA concentrations obtained by a reference method. The new direct in situ transesterification method is robust and simple. Sample preparation time and analysis costs are reduced to a minimum. This method is an economically and ecologically superior alternative to conventional methods for assessing plasma FA status in large studies.

Assay of labile estrogen o-quinones, potent carcinogenic molecular species, by high performance liquid chromatography-electrospray ionization tandem mass spectrometry with phenazine derivatization

A sensitive and selective assay method for labile estrogen o-quinones, estrone (E(1))-2,3-quinone (Q), E(1)-3,4-Q, estradiol (E(2))-2,3-Q and E(2)-3,4-Q, based on the use of phenazine (Phz) derivatization with o-phenylenediamine and high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) was described. The Phz derivatives of four estrogen o-quinones were purified by solid phase extraction and analyzed by HPLC-ESI-MS/MS. The protonated molecule was observed as a base peak for all Phz derivatives in their ESI-mass spectra (positive mode). In multiple reaction monitoring, the transition from [M+H]+ to m/z 231 was chosen for quantification. Calibration curves for the o-quinones were obtained using standard catechol estrogens after sodium metaperiodate treatment and Phz derivatization. Using this method, these four estrogen o-quinones were analyzed with the limit of quantification of 5 ng/ml in acetonitrile (MeCN)-blank matrix (1:4, v/v), respectively, on a basis of the weight of catechol estrogens. Assay accuracy and precision for four estrogen o-quinones were 89.6-113.0% and 3.1-12.6% (5, 125 and 2000 ng/ml in MeCN-blank matrix). Applications of this method enabled to determine the catalytic activities on hydroxylation and subsequent oxidation of E(1) and E(2) of Mushroom tyrosinase and rat liver microsomal fraction. It was confirmed by this method that tyrosinase exhibited 2- and 4-hydroxylation and further oxidation activities for catechols in the ring-A of estrogens. Whereas rat liver microsomal fraction possessed only 2- and 4-hydroxylation activities, and further oxidation activity for catechol estrogens was low.

Proteomic analysis of pancreatic secretory trypsin inhibitor/tumor-associated trypsin inhibitor from urine of patients with pancreatitis or prostate cancer

The development of proteomic methods, especially mass spectrometry, has brought new possibilities to tumor marker research. Pancreatic secretory trypsin inhibitor (PSTI), a common known biomarker for various malignancies, occurs on genetic variants that we are able to detect at the protein level with proteomic techniques using immunoaffinity capture prior to liquid chromatography-mass spectrometry (LC-MS). We also show that PSTI can be detected in urine from cancer patients using a two-step peptide enrichment technique and LC-MS. These results show that tumor-associated peptides can be detected in urine by proteomic techniques.

Thermal melting studies of ligand DNA interactions

A simple thermal melting experiment may be used to demonstrate the stabilization of a given structure by a ligand (usually a small molecule, sometimes a peptide). Preparation of the sample is straightforward, and the experiment itself requires an inexpensive apparatus. Furthermore, reasonably low amounts of sample are required. A qualitative analysis of the data is simple: An increase in the melting temperature (T(m)) indicates preferential binding to the folded form as compared to the unfolded form. However, it is perilous to derive an affinity constant from an increase in T(m) as other factors play a role.

Determination of equilibrium association constants of ligand-DNA complexes by electrospray mass spectrometry

Electrospray mass spectrometry can be used to detect ligand-DNA noncovalent complexes formed in solution. This chapter describes how to determine equilibrium association constants of the complexes. Particular attention is devoted to describing how to tune an electrospray mass spectrometer using a 12-mer oligodeoxynucleotides duplex in order to perform these experiments. This protocol can then be applied to any nucleic acid structure that can be ionized with electrospray mass spectrometry.

In-depth analysis of protein phosphorylation by multidimensional ion exchange chromatography and mass spectrometry

Protein phosphorylation controls fundamental biological functions that are often deregulated in disease. Therefore, system-level understanding of complex pathophysiological processes requires methods that can be used to profile and quantify protein phosphorylation as comprehensively as possible. Here we present a detailed protocol to enrich phosphopeptides from total cell lysates in a form amenable to downstream analysis by mass spectrometry. Using these techniques, we have detected several thousands of phosphorylation sites in the NIH-3T3 cell line.

Quantification of protein kinase activities by LC-MS

Measuring the enzymatic activity of protein kinases in cell and tissue extracts represents a difficult task owing to the complex regulation and dynamics of such enzymes. Here we describe a sensitive and specific approach for the quantitative analysis of PI3K-dependent protein kinase activity based on the mass spectrometry measurement of reaction products. The principle of this method can be applied to develop other kinase assays and thus should contribute to the understanding of processes controlled by protein kinases. Because of the enhanced sensitivity of this technique, it may be applied to the multiplex measurement of pathway activities when sample amounts are limiting.

A method for small molecule microarray-based screening for the rapid discovery of affinity-based probes

We describe herein a new method for the high-throughput identification of affinity-based probes (AfBPs) using a small molecule microarray (SMM) approach. A hydroxylethylene-based small molecule library was first generated by solid-phase combinatorial synthesis. The library was tagged with biotin to facilitate immobilization on avidin-coated slides. Preliminary screening with γ-secretase (both the recombinantly purified protein as well as cellular lysates overexpressing the enzyme) was carried out, in order to identify potential small molecule binders, which were subsequently redesigned into AfBPs. Several specific and potent probes for γ-secretase were thus identified through the binding profiles observed on the SMMs. The SMM platform was able to sensitively and conveniently report activity-based binding interactions between aspartic proteases and their small molecule inhibitors. This new approach thus provides a potentially more rapid and efficient method for developing AfBPs using SMMs.

Urinary proteome profiling using 2D-DIGE and LC-MS/MS

Proteomic methodologies have been at the forefront of cancer research for several years. The use of proteomic strategies to study all expressed genes aims to discover biomarkers indicative of the physiological state of cancer cells at specific time points, enabling early diagnosis, following cancer development/progression, screening and monitoring the efficacy of new therapeutic agents. Onco-proteomics has the potential to impact on oncology practice by delivering individualised highly selective clinical care. 2D-DIGE (2D difference in gel electrophoresis) enables simultaneous examination and comparison of multiple samples using cyanine dyes to label amino acid residues that are then separated based on charge and mass. These advantages combined with universal availability have until recently made 2D-DIGE a first method of choice in cancer proteome analysis of diverse specimens, including tissues, cell lines, blood and other body fluids.

SPR/MS: recovery from sensorchips for protein identification by MALDI-TOF mass spectrometry

Surface plasmon resonance is widely used to study binding interactions with proteins, potentially yielding information on kinetics, thermodynamics and active concentrations. However, the technology cannot identify the involved interaction partners. Mass spectrometry, on the other hand, can be used for specific identification of proteins in amounts comparable to the levels that can be captured on a Biacore SPR sensorchip. Here we present protocols for capturing, washing and eluting proteins from Biacore instruments as well as for robust sample preparation for sensitive mass spectrometric identification.

Application of free flow electrophoresis to the analysis of the urine proteome

Urine is a complex fluid, which is thought to contain valuable diagnostic information regarding general health. In particular, there is great diagnostic potential in the peptide and/or protein content of urine, but the information is present in low abundance. Most traditional proteomic techniques lack sufficient sensitivity/dynamic range, especially for dilute and/or complex samples. However, orthogonal separation methods can be applied prior to protein/peptide analysis to increase the success rate of urine proteomic studies and access this potentially valuable information. In this chapter, we describe isoelectric focusing (IEF) of intact urine proteins, via free flow electrophoresis (FFE), prior to typical peptide-based mass spectrometry analysis, facilitating the deep analysis of urine protein detection and identification, for biomarker discovery. Our work demonstrates that such an approach can be used as a preprocessing step and can be integrated into a workflow for the successful identification of protein components (biomarkers) from urine.

Detection of adriamycin-DNA adducts by accelerator mass spectrometry

There have been many attempts in the past to determine whether significant levels of Adriamycin-DNA adducts form in cells and contribute to the anticancer activity of this agent. Supraclincal drug levels have been required to study drug-DNA adducts because of the lack of sensitivity associated with many of the techniques employed, including liquid scintillation counting of radiolabeled drug. The use of accelerator mass spectrometry (AMS) has provided the first direct evidence of Adriamycin-DNA adduct formation in cells at clinically relevant Adriamycin concentrations. The exceedingly sensitive nature of AMS has enabled over three orders of magnitude increased sensitivity of Adriamycin-DNA adduct detection (compared to liquid scintillation counting) and has revealed adduct formation within an hour of drug treatment. The rigorous protocol required for this approach, together with many notes on the precautions and procedures required in order to ensure that absolute levels of Adriamycin-DNA adducts can be determined with good reproducibility, is outlined in this chapter.

The morphology and lattice structure of bone crystal after strontium treatment in goats

Strontium (Sr) compounds have become increasingly popular in osteoporosis treatment. As a bone seeking element, 98% of Sr deposits in bone and teeth after oral ingestion. However, the quality of new bone after Sr deposition is yet to be extensively investigated. In this study, eight osteopenic goats were divided into two groups: Ca + 40Sr (five goats) and controls (three goats). Controls were fed with low calcium feeds. Ca phosphate was supplied at 100 mg/(kg day), and Sr phosphate at 40 mg/(kg day) in the Ca + 40Sr group. The newly formed bone at the outer cortical area of the femur with Sr deposition was identified from tetracycline labels, and the morphology and lattice structure of the crystals in these regions were investigated. Results showed that Sr concentrations of bone tissue significantly increased 144.37% for Sr administration without significant change in Ca concentration, and the ingested Sr mainly deposited in new bone. The crystal isolated from new bone exhibited the typical character of biological apatite as determined by Fourier transform infrared spectroscopy and selected-area electron diffraction. Transmission electron microscopy examination showed that a crystal with width of 8-10 nm grew along with the (002) lattice and aligned with the same direction in both groups. The elemental analysis of crystals showed that the ingested Sr deposited mainly in the bone matrix or was absorbed on the bone crystal surface, while only a limited amount of Sr replaced Ca in apatite crystals. Our findings showed that Sr administration at current dosages for prevention and treatment of osteoporosis might not change the bone crystal morphology and structure.

Mapping of phosphorylation sites by LC-MS/MS

Reversible protein phosphorylation ranks among the most important post-translational modifications that occurs in the cell. It is therefore highly relevant to elucidate the phosphorylation states of a given biological system, albeit challenging. Most notably the often low stoichiometry of phosphorylation is inherently incompatible with standard LC-MS analysis of a complex protein digest mixture, primarily due to the relative low dynamic range of current mass analyzers. Therefore a need for specific enrichment of phosphorylated peptides or proteins exists. Significant progress surrounding the biochemical analysis of reversible protein phosphorylation in the past years has led to the development of several new techniques to isolate or enrich phosphopeptides, particularly in large-scale analyses. This chapter deals with three such examples.

A review of experimental design best practices for proteomics based biomarker discovery: focus on SELDI-TOF

Surface Enhanced Laser/Desorption Ionization-time of flight (SELDI-TOF) mass spectrometry is a technique uniquely suited to the study of the urine proteome due to its salt tolerance, high-throughput, and small sample requirements. However, due to the extreme sensitivity of the technique, sample collection and storage conditions, as well as instrument protocols and analysis conditions, must be rigorously controlled to ensure that data generated and collected is accurate and free from artifacts. Robust and reproducible data sets can be generated and compared between clinical sites when experimental protocols are carefully standardized. This chapter aims to review known factors that cause irreproducible results so that the experiments may be designed with appropriate sample and process controls for successful biomarker discovery. A suggested protocol follows the review. A number of issues for study design are discussed and these are generally applicable to biomarker discovery experiments.

Urine proteomic analysis: use of two-dimensional gel electrophoresis, isotope coded affinity tags, and capillary electrophoresis

The identities and abundance levels of proteins excreted in urine are not only key indicators of diseases associated with renal function but are also indicators of the overall health of individuals. Urine specimens are readily available and provide a noninvasive means to assess and diagnose many disease states. Proteins in urine originate from two sources: the ultrafiltrate of plasma, and those that are shed from the urinary tract. The protein concentration in urine excreted from a normal adult is approximately 150 mg/day, and is typically not greater than 10 mg/100 mL in any single specimen. Following precipitation, concentration, and fractionation methods, proteins of interest from urine samples can be separated, identified, and quantified. One of the most commonly used techniques in the field of urine proteomics is gel electrophoresis followed by identification with mass spectrometry and protein database search algorithms. In this chapter, two-dimensional gel electrophoresis (2-DE) will be discussed, along with less frequently applied techniques, such as isotope coded affinity tags (ICAT) and capillary electrophoresis (CE). Publications discussing the application of these techniques to urine proteomic analyses of healthy individuals and urinary disease biomarker discovery will also be summarized.

Micro contactor based on isotachophoretic sample transport

It is demonstrated how isotachophoresis (ITP) in a microfluidic device may be utilized to bring two small sample volumes into contact in a well-controlled manner. The ITP contactor serves a similar purpose as micromixers that are designed to mix two species rapidly in a microfluidic channel. In contrast to many micromixers, the ITP contactor does not require complex channel architectures and allows a sample processing in the spirit of "digital microfluidics", i.e. the samples always remain in a compact volume. It is shown that the ITP zone transport through microchannels proceeds in a reproducible and predictable manner, and that the sample trajectories follow simple relationships obtained from Ohm's law. Firstly, the micro contactor can be used to synchronize two ITP zones having reached a channel at different points in time. Secondly, fulfilling its actual purpose it is capable of bringing two samples in molecular contact via an interpenetration of ITP zones. It is demonstrated that the contacting time is proportional to the ITP zone extension. This opens up the possibility of using that type of device as a special type of micromixer with "mixing times" significantly below one second and an option to regulate the duration of contact through specific parameters such as the sample volume. Finally, it is shown how the micro contactor can be utilized to conduct a hybridization reaction between two ITP zones containing complementary DNA strands.

Arsenic speciation in freshwater fish: focus on extraction and mass balance

Arsenic (As) speciation in muscle tissues of freshwater fish was investigated with special emphasis on extraction yields and mass balances. For the quantification of water-soluble As compounds, samples were extracted using a 1:1 (v/v) methanol/water mixture. Various extraction parameters, such as extraction volume, number of additional extractions, intermediate and final volume in sample preconcentration were optimized so as to improve the extraction efficiency. Arsenic compounds were determined by HPLC with online ICP-MS, using both cation and anion exchange separation. The species studied were eel (Anguilla anguilla L.), flathead grey mullet (Mugil cephalus L.), chub (Leuciscus cephalus L.), and carp (Cyprinus carpio L.). Mean total As concentrations ranged from 354 microg kg(-1) dry weight (carp) to 1804 microg kg(-1) dry weight (mullet). Under optimized conditions, the percentage of total As extracted ranged from 64% for carp, to 82%, 84%, and 89% for grey mullet, eel and chub, respectively. Extraction of lipid-rich eel with n-hexane recovered some additional 3% of total As. The sizeable effect of sample matrix on HPLC retention time of some organoarsenicals in gradient elution cation exchange chromatography was exploited to achieve separation of coeluting compounds by analysing the same sample at different dilutions. The recovery of As from chromatographic columns was 101%, 102%, 103% and 104% for carp, chub, mullet and eel, respectively, indicating that no As was retained during chromatography. Arsenobetaine (AB) was the dominating As compound, but several other arsenicals, including arsenous acid (Asiii), arsenic acid (Asv), methylarsonic acid (MMA), dimethylarsinic acid (DMA), trimethylarsine oxide (TMAO), arsenocholine ion (AC), tetramethylarsonium ion (TETRA), oxo-arsenosugar-glycerol (AS1), oxo-arsenosugar-phosphate (AS2), oxo-arsenosugar-sulfate (AS4), thio-arsenosugar-phosphate (ThioAS2), and three unknown As compounds, were found. Arsenic speciation in carp was different compared to the other fish species, and a lower proportion of AB along with a high contribution of AS2 and ThioAS2 was found. DMA and TMAO were noteworthy minor compounds in eel and carp, respectively. Arsenic speciation and the chemical composition of fish muscle both appeared to affect the extraction yield.