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Coated microwell plate-based affinity purification of antigens.

Antibody-based affinity capture of antigens is widely used in the isolation of antigens from complex mixtures. Antibody and the corresponding antigen are allowed to interact with each other to form immunocomplexes which are then typically captured by protein A or protein G immobilized on beaded support. Antigen capture performed using this method generally requires multiple centrifugation steps and careful pipetting to avoid loss of the bead-bound complexes. This traditional procedure is tedious and not easily reproducible, especially when working with multiple samples. To address these issues we have demonstrated that antigens can be captured with protein A/G, protein G, and high binding-capacity streptavidin 96-well strip-coated plates. The coated plate method of antigen purification is reproducible, within the same experiment and between experiments, due to the uniform binding capacity of the plates and wells. Here we report the use of coated microwell plates for antigen capture and for protein-protein interaction studies with the well-characterized BIR2-SMAC, transferrin receptor/ transferrin, and other systems.

Antibody Affinity↗

An excised patch membrane sensor for arachidonic acid released in mouse hippocampal slices under stimulation of L-glutamate.

An excised patch membrane sensor for arachidonic acid (AA) is described, whose response stems from AA-induced channel-type transport of ions across the excised patch membrane. The patch membrane sensor was prepared in situ by excising mouse hippocampal cell membranes with patch pipets having a tip diameter of < 0.5 microm. The sensor responds to AA, giving rise to a channel-type current, and its magnitude (apparent conductance) increased with increasing AA concentration in the range from 10 to 30 nM. The detection limit was 2.1 nM (S/N = 3). The induction of channel-type currents was selective to AA over fatty acids such as palmitic acid, stearic acid, oleic acid, gamma-linolenic acid, and docosahexaenoic acid and AA metabolites such as 12-HETE, 5-HETE, and prostaglandin D(2). The sensor was applied to quantification of AA released from various neuronal regions (CA1, CA3, and DG) of mouse hippocampus under stimulation of 100 microM L-glutamate. The release of AA from each region was observed 1 min after the stimulation and the concentration of AA 5 min after the stimulation varied among the neuronal sites, i.e., 8+/-1 nM (n = 5) for CA1, 15+/-3 nM (n = 3) for CA3, and 6+/-2 nM (n = 9) for DG. The L-glutamate-evoked release of AA was partly inhibited by ionotropic glutamate receptor antagonists (APV and DNQX) and completely blocked by phospholipase A2 (PLA2) inhibitor (MAFP), suggesting that the release of AA occurred by glutamate receptor-mediated activation of PLA2. The potential use of the present sensor for detecting local concentration of AA at various neuronal sites is discussed.

Animals↗

Development of water buffalo (Bubalus bubalis) embryos from in vitro matured oocytes reconstructed with fetal skin fibroblast cells as donor nuclei.

The present study was carried out to explore the feasibility of using buffalo fetal skin fibroblasts as donor nuclei and to find out the developmental competence of embryos following transfer of these nuclei to in vitro matured enucleated buffalo oocytes. Skin cells were isolated from 1 to 2-month-old fetuses obtained from slaughterhouse, by enzymatic digestion (0.5% w/v trypsin +0.05% w/v collagenase in Dulbecco's PBS) for 15-20 min. The cells were washed 4 times with Dulbecco's PBS and then once with RPMI-1640+10% FBS by centrifugation at 600 x g. The cells were then cultured in the same medium in a CO2 incubator (5% CO2 in air) at 38.5 degrees C for 2-3 days. Cumulus-oocyte complexes (COCs) collected from slaughterhouse buffalo ovaries were subjected to IVM in the IVM medium (TCM-199 + 5 microg/ml FSH-P + 10 microg/ml LH+10% FBS) for 20-22 h in a CO2 incubator (5% CO2 in air) at 38.5 degrees C. Oocytes were denuded with 0.1% trypsin followed by repeated pipetting and then enucleated by aspirating the first polar body with 10-15% of nearby cytoplasm with a micromanipulator. Two different types of donor cells (growing cells and those arrested with cytochalasin-B) were used for reconstruction of oocytes. The reconstructs were electro fused and incubated in the activation medium (TCM-199 + 8 microg/ml cytochalasin-B+10% FBS) for 4 h. These were then cultured in IVC medium (TCM-199+10% FBS) in a CO2 incubator (5% CO2 in air) at 38.5 degrees C for 48 h. The cleaved embryos were then co-cultured with buffalo oviduct cells in embryo development media (EDM). Out of 119 denuded matured oocytes which were enucleated and reconstructed with growing cells, 78 (65.5%) were electro fused, activated and cultured, out of which 4 (5.1%) reconstructs cleaved and developed to 2-cell stage, 3 (3.8%) reached to 4-cell stage and 3 (3.8%) reached to 8-cell stage. In the synchronized group, out of 62 denuded matured oocytes which were reconstructed with cytochalasin-B blocked cells, 40 (65%) were electrofused, activated and cultured, out of which 4 (10%) developed to 2-cell stage, 3 (7.50%) to 4-cell stage, 2 (5.0%) to early morula stage and 1 (2.50%) to blastocysts stage. These results suggest that buffalo fetal skin fibroblasts could be used as donor nuclei for the production of buffalo embryos after nuclear transfer to enucleated in vitro matured buffalo oocytes.

Animals↗

Design and evaluation of a grapevine pruner for biofungicide application.

Eutypa lata is a significant grapevine pathogen with limited means of prevention and control. The biological control agent Fusarium lateritium can prevent E. lata infection if applied directly onto a vine pruning wound. F. lateritium was suspended and stored in an invert emulsion formulation. A commercially available pruning shear was modified to dispense the formulated F. lateritium onto the cutting blade for direct application onto the pruning wound simultaneously with grapevine cutting. The modified pruner was tested for its ability to cover grapevine pruning wounds using the emulsion formulation. Efficacy of formulated F. lateritium on pruned grapevine canes was also studied using the pruner for application. Addition of grooves in the pruning blade significantly improved wound coverage. Biological efficacy testing determined that applying formulated F. lateritium with the modified pruner was as effective as pipetting formulation directly onto the pruning wound.

Agriculture↗

A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain.

A low-density oligonucleotide array approach based on the hybridization of consensus PCR products of LSU rDNA was developed in order to simultaneously detect various harmful algae. A set of oligonucleotide probes for the hybridization of specific LSU rDNA D2 regions was developed for the identification of 10 representative harmful microalgae. Each probe was spotted onto a streptoavidin-coated glass slide by pipetting. Universal primers were designed within the conserved regions adjacent to the D2 regions of all harmful algae and used to PCR amplify the complete D2 regions. The PCR products were hybridized to the oligonucleotides arrayed on the slide. The array produced unique hybridization patterns for each species of harmful algae and allowed us to differentiate the closely related species. Furthermore, we were able to simultaneously detect several predominant HAB species from a mixture of culture strains and from a natural sample. These results show that DNA microarray can be a new technical platform for parallel discrimination of harmful algae and has great potential to alter the manner in which researchers monitor these microorganisms.

Consensus Sequence↗

Standardization of calibration and quality control using surface enhanced laser desorption ionization-time of flight-mass spectrometry.

BACKGROUND: Protein profiling by surface enhanced laser desorption ionization-time of flight-mass spectrometry (SELDI-TOF-MS) is gaining importance as a diagnostic tool for a whole range of diseases. This report describes a QC procedure, which acts prospectively by checking the calibration before starting profiling experiments. METHODS: A well-defined protocol for calibration of the Protein Biosystem IIc instrument was established, using a commercial QC sample containing independent certified standards and by determination of acceptance criteria. Instrument calibration was performed externally every week with the standards provided by the manufacturer. QC was performed for the period of 5 months. RESULTS: According to the acceptance criteria defined in this study, data points should be in the established range of the process mean+/-2 standard deviations for the mass-to-charge ratios (m/z values), peak intensities, signal-to-noise ratios (S/N), and peak resolutions for insulin and apomyoglobin in the QC sample. Moreover, it was demonstrated that the pipetting variability in the handling of the QC sample significantly contributed to systematic errors and that spotting of a larger volume of QC sample resulted in a better reproducibility. CONCLUSIONS: Stringent quality control of the calibration part of SELDI-TOF-MS experiments prevents unreliable data acquisition from the very start.

Apoproteins↗

Angiogenic activity of swine granulosa cells: effects of hypoxia and vascular endothelial growth factor Trap R1R2, a VEGF blocker.

The possible role played by hypoxia and vascular endothelial growth factor (VEGF) in the regulation of follicular angiogenesis was studied in a three-dimensional fibrin gel model. Granulosa cells from follicles >5mm were subjected to normoxia (19% O2), partial (5% O2) or total (1% O2) hypoxia and their culture media were collected and used to stimulate porcine Aortic Endothelial Cells (AOC) included in the fibrin matrix. A suspension of AOC on microcarrier beads was pipetted in a fibrinogen solution (1 mg/ml PBS) before the addition of 1250 IU thrombine (250 microl) to catalize the gel formation. Granulosa cell conditioned media were tested in the presence or absence of VEGF Trap R1R2 (150 ng/ml), a potent VEGF inhibitor, that had its efficacy tested by adding VEGF (100 ng/ml) to AOC culture. Endothelial cell proliferation was measured at 48, 96, 144, 192 h by means of Scion Image Beta. A significant (p < 0.01) increase of AOC proliferation at each time of measurement was induced by culture media from granulosa cells subjected to partial (except at the end of the first 48 h) and total hypoxia compared to control and normoxia conditions, and by VEGF. VEGF Trap significantly (p < 0.01) inhibited the stimulatory effect of media conditioned by granulosa cells cultured in hypoxic conditions. These data suggest that hypoxia stimulates angiogenic activity of granulosa cells possibly by means of VEGF which could represent the main effector in promoting endothelial cell proliferation.

Animals↗

Large-scale production of lipoplexes with long shelf-life.

The instability of lipoplex formulations is a major obstacle to overcome before their commercial application in gene therapy. In this study, a continuous mixing technique for the large-scale preparation of lipoplexes followed by lyophilisation for increased stability and shelf-life has been developed. Lipoplexes were analysed for transfection efficiency and cytotoxicity in human aorta smooth muscle cells (HASMC) and a rat smooth muscle cell line (A-10 SMC). Homogeneity of lipid/DNA-products was investigated by photon correlation spectroscopy (PCS) and cryotransmission electron microscopy (cryo-TEM). Studies have been undertaken with DAC-30, a composition of 3beta-[N-(N,N'-dimethylaminoethane)-carbamoyl]-cholesterol (DAC-Chol) and dioleylphosphatidylethanolamine (DOPE) and a green fluorescent protein (GFP) expressing marker plasmid. A continuous mixing technique was compared to the small-scale preparation of lipoplexes by pipetting. Individual steps of the continuous mixing process were evaluated in order to optimise the manufacturing technique: lipid/plasmid ratio, composition of transfection medium, pre-treatment of the lipid, size of the mixing device, mixing procedure and the influence of the lyophilisation process. It could be shown that the method developed for production of lipoplexes on a large scale under sterile conditions led to lipoplexes with good transfection efficiencies combined with low cytotoxicity, improved characteristics and long shelf-life.

Animals↗

Osmotic shock: a mechanosensitive channel blocker can prevent release of cytoplasmic but not periplasmic proteins.

When over-expressed in the cytoplasm of Escherichia coli, carboxylesterase Est55 of Geobacillus stearothermophilus was found to be released from cells upon osmotic shock. Comparing two osmotic shock protocols showed that release of Est55 was abolished in the absence of mechanosensitive channel MscL by one method but not the other. The discrepancy extended to several previously reported cytoplasmic proteins released by osmotic shock, including: EF-Tu, thioredoxin, and DnaK in E. coli. Stepwise analyses of parameters between these two protocols revealed that the use of mechanical pipetting instead of gentle dilution of cells prior to exposure to hypotonic solution abolished the effect of MscL. Furthermore, while this phenomenon of release of certain cytoplasmic proteins was sustained in all three wild type strains of E. coli, presence of gadolinium was able to serve as an MscL channel blocker and prevented release of Est55 and EF-Tu in the process. An optimized protocol of osmotic shock was developed from this study to provide a more reliable assessment of location of proteins in E. coli. This method allowed release of authentic periplasmic MalE and beta-lactamase proteins comparable to that by EDTA-lysozyme treatment.

Biological Transport↗

GHB in postmortem toxicology. Discrimination between endogenous production from exposure using multiple specimens.

Since gamma-hydroxybutyrate (GHB) is present in both blood and urine of the general population as an endogenous compound, toxicologists must be able to discriminate between these endogenous levels and a concentration resulting from exogenous exposure. The implementation of a cut-off concentration must be done cautiously, due to the wide distribution of endogenous concentrations. To verify the accuracy of a proposed 50 mg/l postmortem blood cut-off, we tested 71 autopsy cases of subjects where the cause of death could exclude GHB exposure. The delay between death and autopsy ranged from 12 to 72 h. GHB was tested by gas chromatography-mass spectrometry (GC-MS) after precipitation. Briefly, 20 microl of blood, bile, or vitreous humor was pipetted in a glass tube, followed by 20 microl of GHB-d6 and 45 microl of acetonitrile. After vortexing and centrifugation, the supernatant was collected and evaporated to dryness. The residue was derivatized with bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS) for 20 min at 70 degrees C. After injection on a 30 m HP5 MS capillary column, GHB (m/z 233, 204, and 147) and GHB-d6 (m/z 239) were identified by MS. GHB tested positive in all the 71 whole blood (cardiac) specimens, with concentrations in the range 0.4-409 mg/l, with a major distribution in the range 10-40 mg/l. A concentration >50 mg/l was observed in 14 cases. As there was no data to support GHB exposure, this was considered as postmortem formation. In order to discriminate this contamination, when available, femoral blood, bile or/and, vitreous humor were tested. The following results were obtained: cardiac blood (55-409 mg/l) versus bile (6.1-238 mg/l) in seven cases; cardiac blood (51-409 mg/l) versus femoral blood (17-44 mg/l) in five cases, and cardiac blood (51-409 mg/l) versus vitreous humor (3.9-2 mg/l) in six cases. It is obvious that bile does not fit the requirements for discrimination and that femoral blood and mostly vitreous humor can be of particular interest. These results demonstrate that a positive (>50 mg/l) postmortem blood GHB concentration cannot support alone drug exposure and that it is essential to document the case with other specimens, including peripheral blood and vitreous humor.

Bile↗

Automated high-throughput immunomagnetic separation-PCR for detection of Mycobacterium avium subsp. paratuberculosis in bovine milk.

Two monoclonal antibody-mediated immunomagnetic separation PCR kits (AnDiaTec ParaTub-S IMS-PCR-ELISA and ParaTub-SL IMS-real time PCR) were developed and evaluated for the automated high-throughput detection of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) in bulk milk of naturally infected dairy herds and made commercially available. M. paratuberculosis are first isolated from milk by high-throughput immunomagnetic bead separation using a completely automated magnetic particle pipetting robot within 45 min and released subsequently for analysis directly into PCR amplification mixtures for real time PCR or for PCR-ELISA. The threshold detection level and specificity of the tests were evaluated first with different M. paratuberculosis pure cultures and artificially contaminated (spiked) bulk milk samples. Both experiments proved a good detection limit, specificity and reliability of the tests that consistently detected 20 or less M. paratuberculosis organisms from cattle, deer and mufflon in 1 ml milk. Experiments with more than 200 bulk milk samples that were tested in parallel with the PCR methods and with the cultural method in a second evaluation study demonstrated that both PCR tests are superior to culture and sufficiently sensitive to detect single shedders in pooled milk samples. The experiments proved that the newly developed tests are sensitive, specific and fast, and thus for the first time allow the standardized large-scale routine M. paratuberculosis screening of bulk milk samples at acceptable costs.

Animals↗

Carbon nanotubes as adsorbent of solid-phase extraction and matrix for laser desorption/ionization mass spectrometry.

A method with carbon nanotubes functioning both as the adsorbent of solid-phase extraction (SPE) and the matrix for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) to analyze small molecules in solution has been developed. In this method, 10 microL suspensions of carbon nanotubes in 50% (vol/vol) methanol were added to the sample solution to extract analytes onto surface of carbon nanotubes because of their dramatic hydrophobicity. Carbon nanotubes in solution are deposited onto the bottom of tube with centrifugation. After removing the supernatant fluid, carbon nanotubes are suspended again with dispersant and pipetted directly onto the sample target of the MALDI-MS to perform a mass spectrometric analysis. It was demonstrated by analysis of a variety of small molecules that the resolution of peaks and the efficiency of desorption/ionization on the carbon nanotubes are better than those on the activated carbon. It is found that with the addition of glycerol and sucrose to the dispersant, the intensity, the ratio of signal to noise (S/N), and the resolution of peaks for analytes by mass spectrometry increased greatly. Compared with the previously reported method by depositing sample solution onto thin layer of carbon nanotubes, it is observed that the detection limit for analytes can be enhanced about 10 to 100 times due to solid-phase extraction of analytes in solution by carbon nanotubes. An acceptable result of simultaneously quantitative analysis of three analytes in solution has been achieved. The application in determining drugs spiked into urine has also been realized.

Adsorption↗

Rapid high-yield mRNA extraction for reverse-transcription PCR.

Reverse-transcription PCR (RT-PCR) is the gold standard for mRNA quantification. Efficient, rapid, and high-throughput mRNA extraction is a prerequisite to ensure PCR sensitivity and precision, particularly for quantification of low-abundance mRNAs, and for large numbers of samples. Many mRNA extraction methods entail meticulous handling of individual samples, and are not well suited for large sample numbers. To achieve simple separation of mRNA binding matrix and the medium from which mRNA is to be isolated, oligo (dT)(20)-coated silica beads were used. Simple centrifugation and decanting steps can be used throughout the extraction procedure to separate supernatant fluids from the silica beads. DNase treatment reduced clumping of sedimented beads, thus facilitating bead resuspension and avoiding repeated agitation. DNase treatment also significantly reduced contaminating DNA, increased mRNA purity, and enhanced mRNA PCR readout by approximately 5-fold. The number of target transcripts per sample aliquot was higher in DNase-treated mRNA than in non-treated mRNA or in total nucleic acids. Thus, use of DNase-treated mRNA increased sensitivity of detection and quantification of low-copy transcripts. In conclusion, we describe here a simple, rapid, and cost-effective method that facilitates convenient extraction of high-quality mRNA by minimizing cumbersome mechanical disruption and pipetting steps.

Animals↗

High-throughput protein digestion by trypsin-immobilized monolithic silica with pipette-tip formula.

Based on the monolithic silica gel materials with hierarchical pore structure and on the SPE devices (MonoTip) developed thereof, a trypsin-immobilized monolithic silica in a pipette tip (MonoTip Trypsin) suitable for digesting proteins has been newly developed. The surface of monolithic silica fixed into the tip was chemically modified with trypsin via an aminopropyl group. Trypsin-immobilized monolith successfully performed a rapid digestion of reduced and alkylated proteins with only a few times pipetting operation for the pre-treatment procedure of chromatographic analysis. The novel solid-phase digestion tool using monolithic silica allows a high-throughput trypsin proteolysis of bio-substances in proteomics.

Chromatography, High Pressure Liquid↗

Automated online liquid chromatographic/mass spectrometric metabolic study for prodrug stability.

In vitro metabolic stability studies are performed routinely in drug discovery to determine the rate of metabolism as well as the metabolic fate of compounds. These studies are labor intensive, involving incubation of the compound with a biological matrix, sampling at various time points, stopping the reaction, and sample preparation for analysis. All of these steps involve manual pipetting in the conventional method. An automated method for in vitro metabolism studies is reported here. The method reduces the time and manual labor required and has other advantages, such as better reproducibility and unattended operation. This method utilizes an autosampler custom configured with cooling and incubation capabilities. The autosampler is programmed to directly inject incubation samples at set time points onto an online extraction column. The extracted sample then enters an analytical column for separation and ultimately the mass spectrometer for detection. The injection has the dual function of stopping the reaction and starting the analysis on the LC-MS. This method was used for the metabolic stability study of a prodrug in plasma and liver S9 fractions of five different species. The stability data from the automated method were similar to those obtained using the conventional method. The potential for this method to increase throughput of metabolic stability studies in drug discovery is demonstrated.

Animals↗

A platform for high-throughput molecular characterization of recombinant monoclonal antibodies.

We describe quantitative characterization of a sample preparation platform for rapid and high-throughput analysis of recombinant monoclonal antibodies (MAbs) and their post-translational modifications. MAb capture, desalting and in situ reduction/alkylation were accomplished by sequential adsorption of analyte to solid phase beads (protein A, reverse-phase) suspended in microtiter plate wells. Following elution and rapid tryptic digestion in the presence of acid-labile surfactant (RapiGest), peptides were fractionated by stepwise elution from reverse-phase pipet tips and the fraction containing Fc N-glycopeptides isolated. Direct quantitative analysis of the relative abundance of peptide glycoforms by MALDI-TOF MS in linear mode closely correlated with normal phase HPLC analysis of fluorophore labeled N-glycans released by PNGaseF.

Adsorption↗

High throughput metabolic stability screen for lead optimization in drug discovery.

A high throughput approach for the determination of in vitro metabolic stability and metabolic profiles of drug candidates has been developed. This approach comprises the combination of a Biomek FX liquid handling system with 96-channel pipetting capability and a custom-designed 96-well format on-line incubator with efficient thermal conductivity. This combination facilitates automated reagent preparation, sample incubation, and sample purification for microsome stability studies. The overall process is both fast and accurate and meets the challenges of high throughput screening for drug discovery. A custom designed, user-friendly computer program has been incorporated for large-scale data processing and report generation. Several applications are discussed that implement this strategy for rapid selection of compounds in early drug discovery.

Animals↗

High-throughput pharmacokinetics screen of VLA-4 antagonists by LC/MS/MS coupled with automated solid-phase extraction sample preparation.

Automation of plasma sample preparation for pharmacokinetic studies on VLA-4 antagonists has been achieved by using 96-well format solid-phase extraction operated by Beckman Coulter Biomek 2000 liquid handling system. A Biomek 2000 robot is used to perform fully automated plasma sample preparation tasks that include serial dilution of standard solutions, pipetting plasma samples, addition of standard and internal standard solutions, performing solid-phase extraction (SPE) on Waters OASIS 96-well plates. This automated sample preparation process takes less than 2 h for a typical pharmacokinetic study, including 51 samples, 24 standards, 9 quality controls, and 3-6 dose checks with minimal manual intervention. Extensive validation has been made to ensure the accuracy and reliability of this method. A two-stage vacuum pressure controller has been incorporated in the program to improve SPE efficiency. This automated SPE sample preparation approach combined with liquid chromatography coupled with the high sensitivity and selectivity of tandem mass spectrometry (LC/MS)/MS has been successfully applied on both individual and cassette dosing for pharmacokinetic screening of a large number of VLA-4 antagonists with a limit of quantitation in the range of 1-5 ng/ml. Consequently, a significant throughput increase has been achieved along with an elimination of tedious labor and its consequential tendency to produce errors.

Animals↗