Protein Precipitation Protocol Research Articles

OPTIMIZATION OF THE DNA EXTRACTION PROTOCOL FROM WOOD SAMPLE BY RESPONSE SURFACE METHODS – CENTRAL COMPOSITE DESIGN

The DNA extraction is one of the first steps and plays animportant role in study on genome of any species on earth. Depending on the purpose and object of study, DNA can be extracted from various tissues.For plants, DNA is usually extracted from the leaves, seeds and young buds, in which these tissues are the best DNA source and can be extracted easily. However, the collection of sample from mature trees, which are generally tall, isdifficult and need more facilities. Consequently, it leads to be limited for the study scope.The proposed solutionis to use a wood tissue instead ofthe leaves, seeds and young due to they are easily collected. The problem is very difficult to extract high quality DNA from the wood tissue (Verbylaite et al., 2010). However, if the extraction of DNA from wood tissue would besuccessful, it would open up many research directions and could turn techniques that seemed unfeasible before into the effective solution. Extracting and analyzing DNA from dried wood and processed wood could be developed to explore the possibility of identifying the species and theirorigin. This could be greatly useful for determining the legality of wood log and wood products, and for deterring trade in illegal wood products (Tsumura et al.,2011). Currently, there are some commercialized kits, enabling DNA extraction from wood more easily,e.g. DNeasy Plant Mini Kit (Qiagen), Nucleospin Plant II (Macherey-Nagel), Genomic DNA Purification Kit (Fermentas) and innuPREP Plant DNA Kit (Analytik Jena). However, the commercial Kitsare expensive. Meanwhile, there are some cheaper methods, applying for DNA extraction from wood successfully, such as SDS method (Edwards et al.,1991; Goodwin and Lee, 1993), protein precipitation protocol (Dellaporta et al., 1983; Fang et al., 1992), especially CTAB method, obtaining with a high DNA concentration (Doyle J and Doyle H., 1987). The DNA extracted by CTAB protocol is less pure; however, they are still suitable to use in molecular biology. The objective of this work was to optimize the conditions of CTAB protocol for DNA extraction from wood. The two parameters centrifugation time and volume ratio of isopropanol to solutions containing DNA that affect the yield and quality DNA were explored using the response surface methodology (RSM). The central composite design (CCD) was used to obtain the experimental design matrix. This approach has limited number of actual experiments performed where as allowing probing into possible interaction between these parameters studied and their effect on quantity and quality DNA.

OP.2B.04] DEVELOPMENT OF AN INNOVATIVE, HIGH THROUGHPUT AND COST-EFFECTIVE UHPLC-MS/MS METHOD FOR THE ASSESSMENT OF THERAPEUTIC ADHERENCE IN PATIENTS WITH “RESISTANT” HYPERTENSION

Objective: Nowadays hypertension affects a large fraction of global population. Moreover, 15–30% of patients show drug-resistance, needing the addition of more drugs; meanwhile, polytherapy often results in poor therapeutic adherence, classified as “pseudo-resistant” hypertension. In this context, Therapeutic Drug Monitoring (TDM) of antihypertensive drugs, which consists in the measurement of drug concentration in biological matrices, may help to discern problems in drug pharmacokinetics/pharmacodynamics from cases of poor therapeutic adherence, also considering that not-pharmacological alternative consists in invasive surgery. It has been hence validated an UHPLC-MS/MS method for simultaneous TDM on plasma samples of ten antihypertensive drugs: amlodipine, atenolol, clonidine, chlortalidone, doxazosin, hydrochlorothiazide, nifedipine, olmesartan, ramipril and telmisartan. Design and method: This method has been validated according to FDA guidelines. 200 μl of sample, standard and quality control, added with 40 μl of internal standard working solution, undergo a simple protein precipitation protocol, followed by drying step, and resulting extracts are resuspended in water:acetonitrile 90:10 (v:v; +0.05% formic acid) and then analyzed through a Shimadzu NexeraX2® UHPLC system coupled with a LCMS-8050® tandem mass detector. The validated method was tested on real samples from patients with RH/pseudo-RH, all giving informed consent. Results: All analytical parameters of the method fitted FDA guidelines for all the analytes. 42 patients have been enrolled (SEAL study). TDM revealed that 55% of patients (n = 23) had detectable concentration of all prescribed drugs (considered fully adherent), 26% (n = 11) resulted partially non-adherent (only part of the prescribed drugs was detectable) and 19% (n = 8) were totally not-adherent (no drugs were detected). Through univariate/multivariate logistic regression, the diastolic pressure and the “white-coat” increase in heart rate resulted the best predictors of poor adherence. Through ROC curve analysis a diastolic pressure over 124 mmHg resulted predictive of total inadherence. Conclusions: TDM can be a gold-standard for evaluating therapeutic adherence and this method results eligible for a clinical routine use. We managed to discern cases of inadherence, preserving some patients from an invasive and expensive surgery.

UPLC–MS/MS method for the simultaneous quantification of anti-HBV nucleos(t)ides analogs: Entecavir, lamivudine, telbivudine and tenofovir in plasma of HBV infected patients

Hepatitis B infection affects two billion people worldwide and 350 million of these are chronically infected. Chronic hepatitis B virus is one of the most important cause of mortality and morbidity worldwide. If it is left untreated, about one-third of affected people will develop progressive and possibly fatal liver disease, like hepatic cirrhosis and primary hepatocellular carcinoma. Currently, five nucleos(t)ide analogs are approved for the treatment of chronic HBV infection. They are: lamivudine, adefovir dipivoxil, telbivudine, entecavir and tenofovir disoproxil fumarate.In this work, we developed and validated an UPLC–Tandem mass spectrometry assay method capable of monitoring lamivudine, telbivudine, tenofovir and entecavir plasma concentrations.Both standards and quality controls (high, medium and low) were prepared in human plasma.Each sample was added with internal standard (5′amino-5′deoxy-thymidine) and then drugs were extracted through a protein precipitation protocol with acetonitrile+0.1% formic acid and then dried. The extracts were resuspended in water and then injected into the chromatographic system. The chromatographic separation was performed on an Acquity UPLC HSS T3 1.8μm 2.1×150mm column, with a gradient of water and acetonitrile, both added with formic acid (0.05%). Accuracy, intra-day and inter-day precision at quality controls levels fitted all FDA guidelines for all analytes, while matrix effects and recoveries resulted stable between samples for each analyte. Finally, we tested this method by monitoring plasma concentrations in 30 HBV+ patients with good results. This simple analytical method could represent a useful tool for the management of anti-HBV therapy.

Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation.

The interest for MS-based biomarker analysis in body fluids is steadily increasing as proteomics methodology translates into clinical laboratories. We describe a method for detection of 5 distinct proteins of low mass and medium to low abundance, which are of interest in anti-doping and clinical analysis. The analytical setup is simple and robust and is suitable for high-throughput instrument configurations.

UPLC–MS/MS method for quantification of the azathioprine metabolites 6-mercaptoguanosine and 6-methylmercaptopurine riboside in peripheral blood mononuclear cells

In the treatment of inflammatory bowel diseases, the use of azathioprine is increasing over the time. It has been demonstrated that the effectiveness of this therapy is modulated by the metabolism of azathioprine, which is mainly exerted by both thiopurine methyl-transferase and inosine triphosphatase enzymes. Several studies reported chromatographic methods to determine the amount of its metabolites in erythrocytes, but there are not reported methods to dose them in peripheral blood mononuclear cells (PBMCs). The development of a method capable to quantify azathioprine nucleoside metabolites in this compartment could give better information on drug penetration and metabolism in the active site. In this work, we validated a new chromatographic method suitable for the monitoring of the two major biologically active ribonucleos(t)ide metabolites of azathioprine in PBMCs: 6-thioguanosine and 6-methyl-mercaptopurine riboside. After PBMCs extraction from blood through separation on density gradient, samples underwent a de-phosphorylation procedure with acid phosphatase (only one aliquot for each sample) and were then treated with a protein precipitation protocol in acetonitrile, followed by UPLC-tandem-mass spectrometry analysis. The calibration curve for each metabolite in PBMC fitted a least squares model (weighed 1/X) from 0.048 to 25ng (r2=0.998).Both accuracy and precision parameters fitted FDA guidelines. We tested this method by monitoring the concentrations of each metabolite in PBMC from eight inflammatory bowel diseases affected patients, receiving azathioprine maintenance therapy with optimal results.

7th International Symposium on Enabling Technologies for Life Sciences (ETP)

7^th International Symposium on Enabling Technologies for Life Sciences (ETP)

A UPLC–MS/MS method for the simultaneous plasma quantification of all isomeric forms of the new anti-HCV protease inhibitors boceprevir and telaprevir

HCV infection affects over 170 milions people in the world. Up to now standard-of-care therapy consisted in ribavirin plus interferon-α 2a or 2b. Recently, two new Direct Acting Antivirals (DAA), inhibitors of NS3 HCV protease, have been developed and approved for the routine use on HCV genotype 1 infected patients: boceprevir and telaprevir. Protease inhibitors show complex pharmacokinetics (strong metabolism of both drugs by CYP3A and drug interactions), they require a TID dosage and, furthermore, they are present in plasma patients in two different isomeric forms. In this work, we developed and validated an UPLC–tandem mass spectrometry assay method capable of monitoring the telaprevir and boceprevir concentrations in plasma, discriminating each isomer of both drugs.Blank plasma used for Standards and QCs preparation, was obtained from blood of healthy donors. The calibration curves for each isomer of telaprevir and boceprevir were linear in a range from 46.87ng/mL to 6000ng/mL and from 23.43 to 3000ng/mL, respectively (mean r2>0.998 for all analytes). QCs at three different concentration were prepared: High, Medium and Low. Each Standard, QC and patient sample was treated with a protein precipitation protocol with a solution containing acidified acetonitrile and Internal Standard (6,7-Dimethyl-2,3-di(2-pyridyl)quinoxaline). An aliquot of supernatant was diluted and then directly analyzed by reverse-phase UPLC–MS/MS. Accuracy (mean 98.47%), intra-day (mean <5.21%) and inter-day (mean <7.57%) precision for telaprevir and boceprevir quality controls fitted all FDA guidelines. All compounds resulted stable in our method conditions and the extraction procedure showed a recovery near to 100%. Finally, we tested this method by monitoring plasma concentrations in 9 HCV+ patients, for each triple combined therapy, with good results. The observed median ratio between S and R isomers for boceprevir and telaprevir were 1.22 (IQR 1.10–1.33) and 1.52 (IQR 1.21–1.67), respectively.The use of this simple assay method could be an important tool for management of HCV-1 DAAs treated patients.

Development and validation of a useful HPLC–UV method for quantification of total and phosphorylated-ribavirin in blood and erythrocytes of HCV+ patients

Ribavirin-induced hemolytic anemia is the main cause of discontinuation of the combination therapy with alpha-interferon-2b and ribavirin for the treatment of hepatitis C virus (HCV) infection. The determination of intracellular ribavirin levels in blood, including the levels of its phosphorylated metabolites, might be useful for predicting ribavirin-induced anemia, which could be caused by the accumulation of these molecules within the erythrocytes. In this work, we simplified and validated a previously developed assay method, to make it suitable for routine monitoring of cellular ribavirin. Whole blood diluted with a five-fold volume of ice-cold distilled underwent a process of acid phosphatase digestion to convert phosphorylated ribavirin metabolites to free ribavirin. The resulting mixture, spiked with an internal standard, was treated with a protein precipitation protocol in acetonitrile, followed by reverse-phase high-performance liquid chromatography analysis. The calibration curve for ribavirin levels in whole blood was linear at concentrations from 625 to 320,000 ng/mL (r(2)=0.998). Accuracy, intra-day and inter-day precision for ribavirin and phosphorylated-ribavirin quality controls were all below 9.0%. We tested this method by monitoring blood ribavirin concentrations in 13 HCV+ patients, receiving alpha interferon-plus ribavirin combination therapy.

Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC‐MS/MS

In order to maximize the number of proteins identified from Hela S3 cell lysate we tested various cell lysis, protein precipitation and digestion protocols. First, we compared three different lysis buffers, two mechanical cell disruption methods and two precipitation methods. Then, we tested six different in-solution digestion protocols, three different in-gel digestion protocols and ten different peptide extraction protocols. The result is a proposal for an optimized protocol to prepare the whole cell lysate samples from HeLa S3 cells.

Characterization of Human Myotubes From Type 2 Diabetic and Nondiabetic Subjects Using Complementary Quantitative Mass Spectrometric Methods

Skeletal muscle is a key tissue site of insulin resistance in type 2 diabetes. Human myotubes are primary skeletal muscle cells displaying both morphological and biochemical characteristics of mature skeletal muscle and the diabetic phenotype is conserved in myotubes derived from subjects with type 2 diabetes. Several abnormalities have been identified in skeletal muscle from type 2 diabetic subjects, however, the exact molecular mechanisms leading to the diabetic phenotype has still not been found. Here we present a large-scale study in which we combine a quantitative proteomic discovery strategy using isobaric peptide tags for relative and absolute quantification (iTRAQ) and a label-free study with a targeted quantitative proteomic approach using selected reaction monitoring to identify, quantify, and validate changes in protein abundance among human myotubes obtained from nondiabetic lean, nondiabetic obese, and type 2 diabetic subjects, respectively. Using an optimized protein precipitation protocol, a total of 2832 unique proteins were identified and quantified using the iTRAQ strategy. Despite a clear diabetic phenotype in diabetic myotubes, the majority of the proteins identified in this study did not exhibit significant abundance changes across the patient groups. Proteins from all major pathways known to be important in type 2 diabetic subjects were well-characterized in this study. This included pathways like the trichloroacetic acid (TCA) cycle, lipid oxidation, oxidative phosphorylation, the glycolytic pathway, and glycogen metabolism from which all but two enzymes were found in the present study. None of these enzymes were found to be regulated at the level of protein expression or degradation supporting the hypothesis that these pathways are regulated at the level of post-translational modification. Twelve proteins were, however, differentially expressed among the three different groups. Thirty-six proteins were chosen for further analysis and validation using selected reaction monitoring based on the regulation identified in the iTRAQ discovery study. The abundance of adenosine deaminase was considerably down-regulated in diabetic myotubes and as the protein binds propyl dipeptidase (DPP-IV), we speculate whether the reduced binding of adenosine deaminase to DPP-IV may contribute to the diabetic phenotype in vivo by leading to a higher level of free DPP-IV to bind and inactivate the anti-diabetic hormones, glucagon-like peptide-1 and glucose-dependent insulintropic polypeptide.

AN APPROACH TO THE CHARACTERIZATION OF A NOVEL THERMOPHILIC BACILLUS THERMOAMYLOVORANS LIPASE

The aim of this work was the purification and tentative characterization of a thermophilic lipolytic enzyme from a thermophilic Bacillus thermoamylovorans strain, isolated from a Galician hot spring. This organism showed high extracellular enzyme activity. The extracellular extract was concentrated using several protein precipitation protocols including ammonium sulfate and organic solvents. Further purification was attempted by hydrophobic interaction chromatography (HIC). Also, identification through mass spectrometry techniques was attempted.

A simple high-performance liquid chromatographic method for the determination of diclofenac in human plasma: application to a comparative bioavailability study

A rapid, sensitive and specific method to quantify diclofenac in human plasma using indomethacin as the internal standard (IS) is described. Samples were extracted using protein precipitation protocol and analyzed by high performance liquid chromatography coupled to ultraviolet detection at 276 nm. Chromatography was performed isocratically with a run time of 8.0 min and the retention time observed for diclofenac and IS was 6.0 and 7.0 min, respectively. The calibration curve was linear over the range 50 - 4,000 ng/ml (r2 > 0.9995). The mean recovery of diclofenac ranged from 88.76 to 99.14% and the limit of quantification was 50 ng/ml. Intrabatch precision and accuracy (%CV) of the method ranged from 0.86 to 7.60%, and 99.34 to 103.8%, respectively. Interbatch precision (%CV) and accuracy ranged from 0.26 to 11.4%, and 92.00 to 105.34%, respectively. This HPLC method was used to determine the relative pharmacokinetics of two diclofenac-cholestyramine 140 mg capsule formulations. The study was conducted using an open, randomized and crossover design with a 1-week washout interval. A single 140 mg dose (equivalent to 70 mg of diclofenac) of each formulation was administered to 26 healthy volunteers (13 males and 13 females) and blood samples were obtained over 12-h interval. The geometric mean of diclofenac-cholestyramine/Flotac ratio was 90.53% for AUC0-12 and 100.22% for Cmax. Since the 90% CI for Cmax and AUCs ratios were all inside the 80 - 125% interval, it was concluded that the diclofenac-cholestyramine test formulation is bioequivalent to Flotac regarding both the rate and the extent of absorption.

Comparison of hydrophilic interaction and reversed‐phase liquid chromatography coupled with tandem mass spectrometric detection for the determination of three pharmaceuticals in human plasma

In the present study, hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) combined with tandem mass spectrometric detection (MS/MS) were evaluated and compared for the determination of donepezil, cetirizine and loratadine in human plasma, in terms of sensitivity and sample preparation procedure. A retention study for the above compounds of various polarities was performed, using both C(18) and silica columns, with several aqueous-organic mobile phase ratios, in order to investigate their retention mechanism profile under HILIC and RPLC. Both chromatographic conditions were compared for chromatographic analysis of plasma samples processed with a liquid-liquid extraction (LLE) method for donepezil determination, resulting in significantly higher sensitivity under HILIC. Furthermore, HILIC and RPLC were compared for direct injection, and novel methods including LLE, solid-phase extraction and protein precipitation protocols were developed. Direct injection technique significantly reduced sample preparation time, increasing at the same time method sensitivity. The current study contributes to broadening the range of analyzable compounds by HILIC-MS/MS to molecules of medium polarity.

Determination of endocannabinoid receptor antagonist SR141716 (rimonabant) in plasma by liquid chromatograph tandem mass spectrometry

SR141716 (rimonabant) is an endocannabinoid receptor antagonist. Endocannabinoids are a class of chemicals that affect neurotransmission via G-protein coupled CB1 (brain) and CB2 (peripheral tissue) receptors. Numerous animal studies have shown that SR141716 binds with the CB1 receptor in the brain, resulting in several biological consequences including reduced alcohol intake and reward as well as reduced food consumption. In this work, an analytical method based on liquid chromatography and electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) has been developed and validated for the quantitative measurement of SR141716 in both human and rat plasma to support the investigation of this compound. A suitable internal standard (AM251) has been chosen and the experimental conditions have been optimized for the separation and detection of singly charged positive ions of SR141716 and the internal standard. A protein precipitation protocol has been developed for extraction of SR141716 and the internal standard from plasma samples. Quantitation was achieved using multiple-reaction-monitoring (MRM) mode for SR141716 ( m/ z 463 → m/ z 363) and the internal standard ( m/ z 555 → m/ z 455) and calibration curve over the concentration range of 5.00–1000 ng/ml was plotted using the peak-area ratio versus the concentration of SR141716 with a LOD and LLOQ of 1.09 and 3.62 ng/ml, respectively. The method developed has been used to analyze SR141716 in rat plasma samples from an animal study.

Combined cup loading, bis(2‐hydroxyethyl) disulfide, and protein precipitation protocols to improve the alkaline proteome of Lactobacillus hilgardii

Despite the large number of papers dealing with bacterial proteomes, very few include information about proteins with alkaline pI's, because of the limits inherent in 2-DE technology. Nonetheless, analyses of in silico proteomes of many prokaryotes show a bimodal distribution of their proteins based on their pI's; the most crowded areas lying between pI 4-7 and 9-11. The aim of the present research was to set up a general, simple, and standardizable 2-DE protocol suitable for studying the alkaline proteome of Lactobacillus hilgardii, a Gram-positive bacillus isolated from wine. The method has also been tested on a Gram-negative bacterium able to degrade aromatic pollutants, Acinetobacter radioresistens S13. Optimization of the method was mainly focused on improving protein extraction and IEF (pI 6-11) separation protocols. Concerning IEF, different methods for sample loading (in-gel rehydration and cup loading), and different reducing agents (DTT and bis(2-hydroxyethyl) disulfide (HED)) were tested and compared. The proposed protocol was found to resolve efficiently alkaline proteins from both of our Lactobacillus and Acinetobacter strains, in spite of their different external layers, thus, enabling a more comprehensive study of their proteomes.

Simple chromatography method for simultaneous determination of dextromethorphan and its main metabolites in human plasma with fluorimetric detection

Dextromethorphan, the innocuous non-narcotic antitussive agent, is the most widely used probe drug to assess CYP2D6 function both in vivo and in vitro. For this reason a simple and selective high performance liquid chromatography method with fluorimetric detection for simultaneous quantitation of dextromethorphan, and its main metabolites in human plasma was developed and validated. The method involved a simple and rapid protein precipitation protocol, using a mixture of ZnSO 4 and methanol. The analysis was performed on a 3 μm, C 18 Tracer Excel 15 cm×0.4 cm i.d. column by gradient elution in which Mobile phase A consisted of potassium dihydrogen phosphate buffer (pH=3, 0.01 M):methanol:tetrahydrofuran (68.5:31:0.5), and mobile phase B consisted of methanol:tetrahydrofuran (93.25:6.75). Linear calibration curves were obtained in the range of 10–500 ng/ml for dextromethorphan, dextrorphan and hydroxymorphinan. The limit of quantitation (LOQ) was 10 ng/ml for each compound. The maximum within and between days precisions were 7.4 and 7.8%, respectively. The accuracies at four different concentration levels ranged from 88.2 to 111.5%. The recoveries were between 88.0 and 108.6%. The assay method was successfully applied to determine dextromethorphan metabolic ratio after an oral dose of 30 mg of dextromethorphan hydrobromide.

High-performance liquid chromatographic analysis of AQ4N, an alkylaminoanthraquinone N-oxide

A simple, highly selective and reproducible reversed-phase high-performance liquid chromatography method has been developed for the analysis of the new anti-cancer pro-drug AQ4N. The sample pre-treatment involves a simple protein precipitation protocol, using methanol. Chromatographic separations were performed using a HiChrom HIRPB (25 cm×4.6 mm I.D.) column, with mobile phase of acetonitrile–ammonium formate buffer (0.05 M) (22:78, v/v), with final pH adjusted to 3.6 with formic acid. The flow-rate was maintained at 1.2 ml min −1. Detection was via photodiode array performed in the UV range at 242 nm and, since the compounds are an intense blue colour, in the visible range at 612 nm. The structurally related compound mitoxantrone was used as internal standard. The validated quantification range of the method was 0.05–10.0 μg ml −1 in mouse plasma. The inter-day relative standard deviations (RSDs) ( n=5) ranged from 18.4% and 12.1% at 0.05 μg ml −1 to 2.9% and 3.3% at 10.0 μg ml −1 for AQ4N and AQ4, respectively. The intra-day RSDs for supplemented mouse plasma ( n=6) ranged from 8.2% and 14.2% at 0.05 μg ml −1 to 7.6% and 11.5% at 10.0 μg ml −1 for AQ4N and AQ4, respectively. The overall recovery of the procedure for AQ4N was 89.4±1.77% and 76.1±7.26% for AQ4. The limit of detection was 50 ng ml −1 with a 100 μl sample volume. The method described provides a suitable technique for the future analysis of low levels of AQ4N and AQ4 in clinical samples.