Precipitation Protocol Research Articles

Precipitate coating on cellulose fibre as sorption medium for selenium preconcentration and speciation with hydride generation atomic fluorescence spectrometry

Lanthanum hydroxide precipitate is for the first time coated onto cellulose fibre and serves as a novel sorption medium for separation and speciation of inorganic selenium. A micro-column packed with precipitate-layer-coated cellulose fibre is incorporated into a sequential injection system for selenite retention from a neutral aqueous solution, which is afterwards stripped with a NaBH 4–NaOH solution as eluent. The hydride generation is actuated by merging the eluate and hydrochloric acid downstream, followed by the detection with atomic fluorescence spectrometry. Total inorganic selenium is derived by pre-reduction of selenate and speciation is estimated by difference. The coated precipitate layer can be used for 150 runs for selenium sorption, offering a clear advantage over the conventional precipitation protocols where a large amount of precipitate is dissolved into a small volume of eluent which might interfere with the detection. With a sample volume of 1.0 mL, an enrichment factor of 9.7 and a detection limit of 9 ng L −1 are obtained in a linear range of 0.05–2.5 μg L −1. A sampling frequency of 24 h −1 is achieved along with a R.S.D. of 1.7% at 0.5 μg L −1 Se(IV). The procedure is validated by analyzing selenium in a reference material GBW 10010 (rice) and a human hair sample. It is further demonstrated by speciation of inorganic selenium in surface water samples by pre-reduction of selenate.

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.

Evaluation of three different protocols of protein extraction for Arabidopsis thaliana leaf proteome analysis by two-dimensional electrophoresis

This work was performed to compare three precipitation protocols of protein extraction for 2-DE proteomic analysis using Arabidopsis leaf tissue: TCA-acetone, phenol, and TCA-acetone-phenol. There were no statistically significant differences in protein yield between the three methods. Samples were subjected to 2-DE in the 5 to 8 pH and 14-80 kDa ranges. The TCA-acetone-phenol protocol provided the best results in terms of spot focusing, resolved spots, spot intensity, unique spots detected, and reproducibility. In all, 93 qualitative or quantitative statistically significant differential spots were found between the three protocols. The 2-DE map of TCA-acetone-phenol extracts presented more resolved spots above 40 kDa, with no pI-dependent differences observed between the three protocols. 54 spots were selected for trypsin digestion, and the peptides were analyzed by MALDI-TOF-TOF MS. After database search using peptide mass fingerprinting, and MS/MS combined search, 30 proteins were identified, the proteins from chloroplastic photosynthetic and carbohydrate metabolism being those most highly represented. From these data, we were able to conclude that each extraction protocol had its main features. Considering this, the workflow of any standard comparative proteomic experiment should include the optimization and adaptation of the protein extraction protocol to the plant tissue and to the particular objective pursued.

Kilogram-Scale Synthesis of a Second-Generation Dendrimer Based on 1,3,5-Triazine Using Green and Industrially Compatible Methods with a Single Chromatographic Step

A kilogram scale, divergent and iterative synthesis of a second generation, triazine dendrimer with 12 protected amines on the periphery using common laboratory equipment is reported. The route benefits from common reaction conditions, inexpensive reagents, and aqueous solvents. From the monomers, the desired product dendrimer--the last uncommitted intermediate that leads to a range of committed, generation three targets--can be obtained in 70% overall yield. Of critical importance in the execution of this divergent synthesis is the differential reactivity of chlorine atoms of trichlorotriazine. The stepwise, nucleophilic aromatic substitution of these atoms with amine nucleophiles is both the basis for the dendrimer growth as well as incorporation of solubilizing piperidine groups. Intermediates are obtained and purified through precipitation and/or extraction protocols with the exception of the final product. Isolation of the target dendrimer requires a single silica gel plug filtration. The purity of this material is assessed at >93%, a level consistent with and/or exceeding other commercially available targets.

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.

Magic-Angle Spinning Solid-State NMR Spectroscopy of Nanodisc-Embedded Human CYP3A4

Cytochrome P450 (CYP) 3A4 contributes to the metabolism of approximately 50% of commercial drugs by oxidizing a large number of structurally diverse substrates. Like other endoplasmic reticulum-localized P450s, CYP3A4 contains a membrane-anchoring N-terminal helix and a significant number of hydrophobic domains, important for the interaction between CYP3A4 and the membrane. Although the membrane affects specificity of CYP3A4 ligand binding, the structural details of the interaction have not been revealed so far because X-ray crystallography studies are available only for the soluble domain of CYP3A4. Here we report sample preparation and initial magic-angle spinning (MAS) solid-state NMR (SSNMR) of CYP3A4 (Delta3-12) embedded in a nanoscale membrane bilayer, or Nanodisc. The growth protocol yields approximately 2.5 mg of the enzymatically active, uniformly 13C,15N-enriched CYP3A4 from 1 L of growth medium. Polyethylene glycol 3350-precipitated CYP3A4 in Nanodiscs yields spectra of high resolution and sensitivity, consistent with a folded, homogeneous protein. CYP3A4 in Nanodiscs remains enzymatically active throughout the precipitation protocol as monitored by bromocriptine binding. The 13C line widths measured from 13C-13C 2D chemical shift correlation spectra are approximately 0.5 ppm. The secondary structure distribution within several amino acid types determined from 13C chemical shifts is consistent with the ligand-free X-ray structures. These results demonstrate that MAS SSNMR can be performed on Nanodisc-embedded membrane proteins in a folded, active state. The combination of SSNMR and Nanodisc methodologies opens up new possibilities for obtaining structural information on CYP3A4 and other integral membrane proteins with full retention of functionality.

Enabling Coupled Quantitative Genomics and Proteomics Analyses from Rat Spinal Cord Samples

Translational research is progressing toward combined genomics and proteomics analyses of small and precious samples. In our analyses of spinal cord material, we systematically evaluated disruption and extraction techniques to determine an optimum process for the coupled analysis of RNA and protein from a single 5-mm segment of tissue. Analyses of these distinct molecular species were performed using microarrays and high resolution two-dimensional gels, respectively. Comparison of standard homogenization with automated frozen disruption (AFD) identified negligible differences in the relative abundance of genes (44) with all genes identified by either process. Analysis on either the Affymetrix or Applied Biosystems Inc. gene array platforms provided good correlations between the extraction techniques. In contrast, the AFD technique enabled identification of more unique proteins from spinal cord tissue than did standard homogenization. Furthermore use of an optimized CHAPS/urea extraction provided better protein recovery, as shown by quantitative two-dimensional gel analyses, than did solvent precipitation during TRIzol-based RNA extraction. Thus, AFD of tissue samples followed by protein and RNA isolation from separate aliquots of the frozen powdered sample is the most effective route to ensure full, quantitative analyses of both molecular entities.

Polyclonal Antibodies from Hen Egg Yolk (IgY) with Hydrolysis Activity

Polyclonal catalytic antibodies (abzymes) play an important role in immunology research. In this study, we report polyclonal antibodies IgYs isolated from chicken egg yolk with hydrolysis activity for the first time. The IgYs were raised in hens using HNPBV [4-(hydroxy (naphthalen-2-yloxy) phosphoryl) butanoic acid] attached to BSA (Bovine serum albumin) as an immunogen. Anti-(HNPBV-BSA) IgYs were isolated from yolks of the eggs laid using a two-step salt precipitation and one-step gel filtration protocol. NA (naphthalen-2-yl acetate) was selected as the substrate and the hydrolysis reaction of the IgYs for it was examined. The result reveals that the rate of the hydrolysis reaction is higher (Kcat/K (uncat) approximately 2x10(4)). The purified IgYs were digested with pepsin and the smaller fragment (Fab') with specific antigen binding properties was produced. The research indicates that the enzymatic properties of Fab' are similar to IgYs. The catalytic activity of the IgYs was further determined by measuring the rate of hydrolysis of NA in the presence of inhibitor. These findings show that chicken egg is an excellent donor for polyclonal catalytic antibodies.

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.

Examination of precipitation chemistry and improvements in precision using the Mg(OH) 2 preconcentration inductively coupled plasma mass spectrometry (ICP-MS) method for high-throughput analysis of open-ocean Fe and Mn in seawater

The chemistry of magnesium precipitation preconcentration of Fe, Mn, and Co from seawater was investigated, and this analytical technique was adapted for use with the Element-2 inductively coupled plasma mass spectrometer (E2 ICP-MS). Experiments revealed that the scavenging efficiency of Mn using the precipitation protocol described here was ∼95% and similar to that previously observed with Fe. In contrast, the scavenging efficiency of Co was three-fold lower than that of Fe and Mn, resulting in poor recovery. An increase in sample size to 13 mL led to several desired effects: (1) an increase in the Fe and Mn signals allowing a final dilution of samples to 0.5 mL and the use of an autosampler, (2) an increase in precision to ∼1–2.5% R.S.D., and (3) an increase in signal relative to the blank. Experiments suggest metal concentration from seawater occurs during the formation of Mg(OH) 2 precipitate, whereas P was scavenged by adsorption onto the Mg(OH) 2 particles. Example vertical profiles are shown for dissolved Fe and Mn from the Equatorial Pacific.

Systematic Evaluation of Sample Preparation Methods for Gel-Based Human Urinary Proteomics: Quantity, Quality, and Variability

We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the greatest protein recovery yield (92.99%), whereas precipitation with 10% acetic acid had the least protein recovery (1.91%). In most of precipitation protocols, the higher percentage of applied organic compounds provided the greater recovery yield. With a fixed concentration at 75%, the urine precipitated with acetonitrile had the greatest number of protein spots visualized in 2D gel, whereas the acetic-precipitated sample had the smallest number of spots. For the intra-individual variability, the first morning urine had the greatest amount of total protein but provided the smallest number of protein spots visualized. Excessive water drinking, not caffeine ingestion, caused alterations in the urinary proteome profile with newly presenting spots and also proteins with decreased excretion levels. As expected, there was a considerable degree of inter-individual variability. Coefficients of variation for albumin and transferrin expression were greatest by inter-individual variables. Male urine had greater amount of total protein but provided smaller number of protein spots compared to female urine. These data offer a wealth of useful information for designing a high-quality, large-scale human urine proteome project.

An evaluation of methods for extraction and quantification of protein from marine macro- and microalgae

Comparison of data of protein content in algae is very difficult, primarily due to differences in the analytical methods employed. The different extraction procedures (exposure to water, grinding, etc.), protein precipitation using different amounts of 25% trichloroacetic acid and quantification of protein by two different methods and using two protein standards were evaluated. All procedures were tested using freeze-dried samples of three macroalgae: Porphyra acanthophora var. acanthophora, Sargassum vulgare and Ulva fasciata. Based on these results, a protocol for protein extraction was developed, involving the immersion of samples in 4.0 mL ultra-pure water for 12 h, followed by complete grinding of the samples with a Potter homogeniser. The precipitation of protein should be done with 2.5:1 25% TCA:homogenate (v/v). The protocol for extraction and precipitation of protein developed in this study was tested with other macroalgae (Aglaothamnion uruguayense, Caulerpa fastigiata, Chnoospora minima, Codium decorticatum, Dictyota menstrualis, Padina gymnospora and Pterocladiella capillacea) and microalgae (Amphidinium carterae, Dunaliella tertiolecta, Hillea sp., Isochrysis galbana and Skeletonema costatum). Comparison with the actual protein content determined from the sum of amino acid residues, suggests that Lowry's method should be used instead of Bradford's using bovine serum albumin (BSA) as protein standard instead of casein. This may be related to the reactivity of the protein standards and the greater similarity in the amino acid composition of BSA and algae. The current results should contribute to more accurate protein determinations in marine algae.

Increased Expression of Mcl-1 Is Required for Protection against Serum Starvation in Phosphatase and Tensin Homologue on Chromosome 10 Null Mouse Embryonic Fibroblasts, but Repression of Bim Is Favored in Human Glioblastomas

Inactivating mutations in the tumor suppressor gene phosphatase and tensin homologue on chromosome 10 (PTEN) result in elevated levels of phosphatidylinositol (3,4,5)-trisphosphate, activation of protein kinase B (PKB), and protection against apoptotic insults such as withdrawal of survival factors. Protection may arise through the inhibition of the pro-apoptotic protein Bim, which is normally repressed by a PKB-dependent mechanism. Here we show that PTEN-/- immortalized mouse embryonic fibroblasts (MEFs) exhibit elevated PKB phosphorylation and are resistant to serum withdrawal-induced death, but exhibit normal Bim expression following withdrawal of serum. In contrast, expression of Mcl-1, a prosurvival member of the Bcl-2 family, was elevated in PTEN-/- MEFs. Transient or stable overexpression of Mcl-1 in PTEN+/- MEFs conferred resistance to serum withdrawal, whereas ablating expression of Mcl-1 in PTEN-/- MEFs, using RNA interference, abolished their resistance to serum withdrawal-induced apoptosis. To determine if Mcl-1 is selected for overexpression in human tumors we examined human glioblastoma cell lines but found that loss of PTEN had no effect on Mcl-1 expression. In contrast, two of three PTEN-/- glioblastoma cell lines exhibited low expression of Bim, which was refractory to serum withdrawal. These results indicate that the resistance of PTEN-/- MEFs to serum withdrawal is largely due to the up-regulation of Mcl-1 but that loss of PTEN in tumor cell lines is more complex and may favor de-regulation of different apoptotic regulators such as Bim.

Ectopic UCP1 gene expression in HepG2 cells affects ATP production

The UCP1 is an uncoupling protein located in the inner mitochondrial membrane of brown adipocytes, which has a well-documented role in diet-induced thermogenesis. The current study assessed whether UCP1 transfected liver cells demand more fuel substrates in the oxidative phosphorylation processes. Therefore, the purpose of this experiment was to achieve an ectopic expression of UCP1 in HepG2 cells to significantly decrease the production of ATP. The UCP1 gene was transferred into the hepatic cells by using a calcium phosphate precipitation protocol. The efficiency of the transfection was tested, 48 hours later, by bioluminescence of luciferase previously transfected, while the expression of mRNA of UCP1 was demonstrated by RT-PCR. In addition, measuring the production of ATP by using a bioluminescence procedure assessed the functionality of this protein. Transfected liver cells with UCP1 showed a decrease of 23% in ATP production in comparison with control cells without expression of UCP1 (2.23 vs. 2.90 RLU/pg protein, p=0.015). In conclusion, the ectopic expression of UCP1 decreased the production of ATP, possibly uncoupling the oxidative phosphorylation, which could be a novel approach for understanding thermogenic processes and eventually for energy metabolism and body weight management.

Molecular Cloning of a Sixth Member of the K+-dependent Na+/Ca2+ Exchanger Gene Family, NCKX6

Bioinformatic and molecular cloning tools were used to identify and isolate cDNA clones from mouse and human tissues that encode the sixth member of the K(+)-dependent Na+/Ca2+ exchanger family, NCKX6. The mouse NCKX6 protein is 585 amino acids long and shares about 62% sequence similarity with previously identified exchangers in the alpha-repeat regions but has little primary sequence similarity outside these regions. NCKX6 transcripts of 4 kb are abundantly expressed in all tissues examined and are thus more broadly distributed than previously described NC(K)X family members. Two alternatively spliced products of this novel gene were identified that encode proteins of different length. The short isoform differs from the full-length isoform at the C-terminal hydrophobic domain as a result of a shift in the reading frame caused by the deletion of two exons. Both NCKX6 isoforms were expressed in HEK-293 cells. Functional analysis by digital imaging of fura-2 loaded transfected HEK-293 cells demonstrated that the short isoform exhibited K(+)-dependent Na+/Ca2+ exchange activity whereas the full-length isoform did not. The latter was retained within the endoplasmic reticulum, whereas the short isoform was present at the plasma membrane in transfected cells. Immunofluorescence studies examining NCKX6 expression in native tissue using an NCKX6-specific antibody showed intense labeling of the cardiac sarcolemmal membrane. The discovery of NCKX6 therefore reveals a novel member of the Na+/Ca2+ exchanger superfamily whose ubiquitous expression in all tissues suggests an important role for K(+)-dependent Na+/Ca2+ exchange in maintaining cellular Ca2+ homeostasis in diverse tissues and cell types.

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.

Improved quantitative real-time RT-PCR for expression profiling of individual cells.

The real-time quantitative polymerase chain reaction (rtqPCR) has overcome the limitations of conventional, time-consuming quantitative PCR strategies and is maturing into a routine tool to quantify gene expression levels, following reverse transcription (RT) of mRNA into complementary DNA (cDNA). Expression profiling with single-cell resolution is highly desirable, in particular for complex tissues like the brain that contain a large variety of different cell types in close proximity. The patch-clamp technique allows selective harvesting of single-cell cytoplasm after recording of cellular activity. However, components of the cDNA reaction, in particular the reverse transcriptase itself, significantly inhibit subsequent rtqPCR amplification. Using undiluted single-cell cDNA reaction mix directly as template for rtqPCR, I observed that the amplification kinetics of rtqPCRs were dramatically altered in a non-systematic fashion. Here, I describe a simple and robust precipitation protocol suitable for purification of single-cell cDNA that completely removes inhibitory RT components without detectable loss of cDNA. This improved single-cell real-time RT-PCR protocol provides a powerful tool to quantify differential gene expression of individual cells and thus could complement global microarray-based expression profiling strategies.

Magnetic bead purification of labeled DNA fragments for high-throughput capillary electrophoresis sequencing.

We have developed an automated purification method for dye-terminator-based DNA sequencing products using a magnetic bead approach. This 384-well protocol generates sequence fragments that are essentially free of template DNA, salt, and excess dye-terminator products. In comparison with traditional ethanol precipitation protocols, this method uses no centrifugation, is rapid, completely automated, and increases the phred-20 read length by an average of 40 bases. To date, we have processed over 4 million samples with 94% averaging 641 phred-20 bases on the MegaBACE 1000 and 4000 and the ABI PRISM 3700 capillary instruments.

Preparation and mass spectrometric study of egg yolk antibody (IgY) against rabies virus.

Rabies virus was used as the antigen to immunize laying chickens. Anti-rabies virus immunoglobulin Y(IgY) was isolated from yolks of the eggs laid by these chickens using a two-step salt precipitation and one-step gel filtration protocol. The purified IgY was reduced with dithiothreitol, and heavy chains (HC) and light chains (LC) were obtained. In addition, the purified IgY was digested with pepsin and the fragment with specific antigen binding properties (Fab) was produced. Using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOFMS), the average molecular weights of IgY, HC, LC, and Fab were determined as 167 250, 65 105, 18 660, and 45,359 Da, respectively. IgY has two structural differences compared with mammalian IgGs. First, the molecular weight of the heavy chain of IgY is larger than that of its mammalian counterpart, while the molecular weight of the light chain of IgY is smaller. Second, upon pepsin digestion, anti-rabies virus IgY is degraded into Fab, in contrast to mammalian IgG, which has been reported to be degraded into F(ab')(2) under the same conditions.

Microgels for estimation of DNA strand breaks, DNA protein crosslinks and apoptosis

This report describes a part of the evolution of microgel electrophoresis in the author’s laboratory for the last 15 years. It also describes the importance of estimation of DNA single and double strand breaks, DNA crosslinks and apoptosis. Some experiments based on each methodology are included here. A new protocol for rapid and efficient precipitation of DNA in microgel is included. A step by step description of laboratory protocol is also included.