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PubMed1990

Capture and penetration processes of the free-living juveniles of Trichostrongylus colubriformis (Nematoda) by the nematophagous fungus, Arthrobotrys oligospora.

The nematode-trapping fungus Arthrobotrys oligospora traps and invades all the free-living juvenile stages of the trichostrongyle nematode Trichostrongylus colubriformis. The processes of capture and invasion of the 1st-stage juveniles are described using differential interference contrast optics and 3-D reconstruction techniques. The adhesive responsible for capture is well preserved using a freeze-substitution technique for scanning electron microscopy. The invasion process of the ensheathed 3rd-stage juvenile of T. colubriformis takes much longer than in the 1st- or 2nd-stage juvenile and involves the formation of secondary infection pegs between the sheath and the cuticle which appear to penetrate the cuticle by physical pressure.

Animals↗

PubMed2003

Spatial and temporal variation of life-history traits documented using capture-mark-recapture methods in the vector snail Bulinus truncatus.

The population biology of the schistosome-vector snail Bulinus truncatus was studied in an irrigation area near Marrakech, Morocco, using demographic approaches, in order to estimate life-history parameters. The survey was conducted using 2 capture-mark-recapture analyses in 2 separate sites from the irrigation area, the first one in 1999 and the second one in 2000. Individuals larger than 5 mm were considered. The capture probability varied through time and space in both analyses. Apparent survival (from 0.7 to 1 per period of 2-3 days) varied with time and space (a series of sinks was considered), as well as a square function of size. These results suggest variation in population intrinsic rate of increase. They also suggest that results from more classical analyses of population demography, aiming, for example at estimating population size, should be interpreted with caution. Together with other results obtained in the same irrigation area, they also lead to some suggestions for population control.

Animals↗

PubMed1992

Laboratory diagnosis of Mycoplasma pneumoniae infection. 4. Antigen capture and PCR-gene amplification for detection of the Mycoplasma: problems of clinical correlation.

Direct detection assays for Mycoplasma pneumoniae were established by PCR amplification of short sequences within the foot protein/adhesin (P1) gene and the 16S ribosomal RNA gene. Specificity and sensitivity was excellent, no hybridization was observed with M. genitalium and other human Mycoplasma species. In nose and throat washings from subjects with respiratory infection a pattern of high counts (c.f.u./ml) of M. pneumoniae (deduced from the amount of amplified PCR product), and a positive antigen capture assay, was found in 83% of subjects with serological evidence of current infection with M. pneumoniae. A small proportion of subjects with serological patterns suggesting infection in the more distant past had positive PCR assays. This was considered to represent either persistence of the organism from a previous infection or perhaps transient carriage during a reinfection, without substantial change in antibody response. PCR-based assay of M. pneumoniae offers a powerful, rapid, and sensitive substitute for culture of the mycoplasma. Antigen capture, while less sensitive than PCR, offers the advantage that it is more often positive with samples from current infection and requires less stringent laboratory organization to contain false positive results. We conclude however that the laboratory diagnosis of a chosen clinical episode should not rest on the PCR or Ag-EIA assays alone, but must also include antibody assays to confirm whether infection is current or represents persistence from past exposure.

Antigens, Bacterial↗

PubMed2003

Repeat capture-recapture studies as part of the evaluation of the surveillance of Legionnaires' disease in France.

We evaluated improvements made to the mandatory notification surveillance system for Legionnaires' disease in France by estimating its sensitivity in 1995 and 1998 using a repeat capture-recapture method. A case of Legionnaires' disease was defined as a person treated for pneumonia in whom legionella had been detected. Patient details were collected from (1) mandatory notifications; (2) the National Reference Centre for Legionella; (3) a postal survey of all hospital laboratories. The three sources were cross-matched and 715 individual cases were identified. A log-linear model, which included an interaction term between mandatory notifications and both the National Reference Centre and Laboratory sources, provided an estimated total of 1124 cases (95% CI 973-1275) in 1998, a twofold increase compared with 1995. The sensitivity of the surveillance system improved from 10% in 1995 to 33% (95% CI 29-38%) in 1998. Capture-recapture methods are important tools in the evaluation of surveillance systems.

Data Collection↗

PubMed2000

Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins.

In previous studies, electron capture dissociation (ECD) has been successful only with ionized smaller proteins, cleaving between 33 of the 153 amino acid pairs of a 17 kDa protein. This has been increased to 99 cleavages by colliding the ions with a background gas while subjecting them to electron capture. Presumably this ion activation breaks intramolecular noncovalent bonds of the ion's secondary and tertiary structure that otherwise prevent separation of the products from the nonergodic ECD cleavage of a backbone covalent bond. In comparison to collisionally activated dissociation, this "activated ion" (AI) ECD provides more extensive, and complementary, sequence information. AI ECD effected cleavage of 116, 60, and 47, respectively, backbone bonds in 29, 30, and 42 kDa proteins to provide extensive contiguous sequence information on both termini; AI conditions are being sought to denature the center portion of these large ions. This accurate "sequence tag" information could potentially identify individual proteins in mixtures at far lower sample levels than methods requiring prior proteolysis.

Amino Acid Sequence↗

PubMed1994

Separation-free sandwich enzyme immunoassays using microporous gold electrodes and self-assembled monolayer/immobilized capture antibodies.

A novel separation-free sandwich-type enzyme immunoassay for proteins is performed by designing an electrochemical detection system that enables preferential measurement of surface-bound enzyme-labeled antibody relative to the excess enzyme-labeled reagent in the bulk sample solution. In this initial model system, the assay is carried out using gold-coated microporous nylon membranes (pore size 0.2 micron) which are mounted between two chambers of a diffusion cell. The membrane serves as both a solid phase for the sandwich assay and the working electrode in the three-electrode amperometric detection system. The capture monoclonal antibody is immobilized covalently on the gold side of the membrane via a self-assembled monolayer of thioctic acid. In the separation-free sandwich assay, both model analyte protein (human chorionic gonadotropin; hCG) and alkaline phosphatase labeled anti-hCG (ALP-Ab) are incubated simultaneously with the immobilized capture anti-hCG antibody. Surface-bound ALP-Ab is spatially resolved from the excess conjugate in the bulk sample solution by introducing the enzyme substrate (4-aminophenyl phosphate) through the back side of the porous membrane. The substrate diffuses rapidly through the porous membrane where it first encounters bound ALP-Ab at the gold surface. The enzymatically generated product, aminophenol, is detected immediately by oxidation at the gold electrode (at +0.19 V vs Ag/AgCl), and the magnitude of current is directly proportional to the concentration of hCG in the sample. The response time after substrate addition is less than 1 min, although maximum response toward the analyte protein requires a sample/conjugate preincubation time of 30 min with the porous electrode.(ABSTRACT TRUNCATED AT 250 WORDS)

Antibodies↗

PubMed2001

Advantages of external accumulation for electron capture dissociation in Fourier transform mass spectrometry.

A combination of external accumulation (XA) with electron capture dissociation (ECD) improves the electron capture efficiency, shortens the analysis time, and allows for rapid integration of multiple scans in Fourier transform mass spectrometry. This improves the signal-to-noise ratio and increases the number of detected products, including structurally important MS3 fragments. With XA-ECD, the range of the labile species amenable to ECD is significantly extended. Examples include the first-time determination of the positions of six GalNAc groups in a 60-residue peptide, five sialic acid and six O-linked GalNAc groups in a 25-residue peptide, and the sulfate group position in a 11-residue peptide. Even weakly bound supramolecular aggregates, including nonspecific peptide complexes, can be analyzed with XA-ECD. Preliminary results are reported on high-rate XA-ECD that uses an indirectly heated dispenser cathode as an electron source. This shortens the irradiation time to > or = 1 ms and increases the acquisition rate to 3 scans/s, an improvement by a factor of 10-100.

Adrenocorticotropic Hormone↗

PubMed2002

Automated affinity capture-release of biotin-containing conjugates using a lab-on-valve apparatus coupled to UV/visible and electrospray ionization mass spectrometry.

We report a new method for automated affinity capture and release of biotin-containing conjugates on immobilized streptavidin using a lab-on-valve (LOV) bead injection apparatus. The apparatus is also coupled to UV/visible and electrospray ionization mass spectrometry (ESI-MS) for monitoring the captured and released biotin-containing conjugates. Dissociation rate constants for release from streptavidin of two chromophore-tagged biotin conjugates were measured by UV/visible spectrometry and the dissociation was simultaneously monitored by ESI-MS. The LOV-ESI-MS instrument was also used for repetitive assays of lysosomal beta-galactosidase in human cell homogenates. Fast analysis in 4.5 min/full cycle and robust operation in 60 repetitive analyses are demonstrated that are promising for transfer of the LOV-ESI-MS technology into clinical practice.

Affinity Labels↗

PubMed2003

Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

In hot electron capture dissociation (HECD), multiply protonated polypeptides fragment upon capturing approximately 11-eV electrons. The excess of energy upon the primary c, z* cleavage induces secondary fragmentation in z* fragments. The resultant w ions allow one to distinguish between the isomeric Ile and Leu residues. The analytical utility of HECD is evaluated using tryptic peptides from the bovine milk protein PP3 containing totally 135 amino acid residues. Using a formal procedure for Ile/Leu (Xle) residue assignment, the identities of 20 out of 25 Xle residues (80%) were determined. The identity of an additional two residues could be correctly guessed from the absence of the alternative w ions, and only two residues, for which neither expected nor alternative w ions were observed, remained unassigned. Reinspection of conventional ECD spectra also revealed the presence of Xle w ions, although at lower abundances, with 44% of all Xle residues distinguished. Using a dispenser cathode as an electron source, identification of four out of five Xle residues in a 2.7-kDa peptide was possible with one acquisition 2 s long, with identification of all five residues by averaging of five such acquisitions. Unlike the case of high-energy collision-induced dissociation, no d ions were observed in the HECD of tryptic peptides.

Amino Acid Sequence↗

PubMed2002

Enhanced affinity capture MALDI-TOF MS: orientation of an immunoglobulin G using recombinant protein G.

Although immobilization of antigen-specific immunoglobulins onto matrix-assisted laser desorption/ionization (MALDI) targets allows the specific detection and enrichment of an antigen from complex biological fluids, the process of antibody immobilization is not optimal. The principal reason is that the antibody can bind to the template in various orientations, many of which block antigen recognition. An affinity capture MALDI mass spectrometry methodology was developed by covalently immobilizing an Fc receptor (recombinant protein G) onto MALDI gold targets for the purpose of orientating an immunoglobulin G, with the Fab domains pointing away from the target surface. The pregnancy and cancer marker, human chorionic gonadotropin beta core fragment (hCGbetacf), was our chosen test substance. To optimize the methodology, different surface densities of protein G and immunoglobulin were achieved by employing varying concentrations for immobilization. Captured amounts of hCGbetacf were compared using an external standard (cytochrome c). Orientation of immunoglobulin resulted in an approximately 3-fold increase in MALDI signal compared to using randomly immobilized antibody. Higher antibody concentrations resulted in diminished MALDI signals, which were explained by steric hindrance. Purification and enrichment of hCGbetacf was achieved from a test solution containing contaminant peptides and proteins using oriented immunoglobulins on-target.

Anisotropy↗

PubMed2003

Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer.

We have mounted a permanent on-axis dispenser cathode electron source inside the magnet bore of a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. This configuration allows electron capture dissociation (ECD) to be performed reliably on a millisecond time scale. We have also implemented an off-axis laser geometry that enables simultaneous access to ECD and infrared multiphoton dissociation (IRMPD). Optimum performance of both fragmentation techniques is maintained. The analytical utility of performing either ECD or IRMPD on a given precursor ion population is demonstrated by structural characterization of several posttranslationally modified peptides: IRMPD of phosphorylated peptides results in few backbone (b- and y-type) cleavages, and product ion spectra are dominated by neutral loss of H3PO4. In contrast, ECD provides significantly more backbone (c- and z*-type) cleavages without loss of H3PO4. For N-glycosylated tryptic peptides, IRMPD causes extensive cleavage of the glycosidic bonds, providing structural information about the glycans. ECD cleaves all backbone bonds (except the N-terminal side of proline) in a 3-kDa glycopeptide with no saccharide loss. However, only a charge-reduced radical species and some side chain losses are observed following ECD of a 5-kDa glycopeptide from the same protein. An MS3 experiment involving IR laser irradiation of the charge-reduced species formed by electron capture results in extensive dissociation into c- and z-type fragment ions. Mass-selective external ion accumulation is essential for the structural characterization of these low-abundance (modified) peptides.

Amino Acid Sequence↗

PubMed2005

Protein capture in silica nanotube membrane 3-D microwell arrays.

The microarray format has allowed for rapid and sensitive detection of thousands of analyte DNAs in a single sample, and there is considerable interest in extending this technology to protein biosensing. While glass is the most common substrate for microarrays, its binding capacity is limited because the glass surface is flat. One way to overcome this limitation is to develop arrays based on porous materials. Such "3-D" arrays can provide greater sensitivity because both the capture molecules and the analyte species they bind are immobilized throughout the thickness of the porous material. We describe here 3-D protein microarrays based on nanopore alumina membranes that contain silica nanotubes within the pores. These microarrays are prepared via a plasma-etch method using a TEM grid as the etch mask and consist of individual nanotube-containing microwells imbedded in a Ag film that coats the alumina membrane surface. We show that the microwells can be functionalized with antibodies and that these antibodies can capture their antigen proteins, which serve as prototype analytes. The analyte proteins are fluorescently tagged, which allows for fluorescence microscopy-based imaging of the array. The Ag surrounding the microwells shows very low background fluorescence, thus improving the signal-background ratio obtained from these arrays.

Electrochemistry↗

PubMed2006

Application of capture-recapture models to estimation of protein count in MudPIT experiments.

MudPIT is an automated shotgun proteomics approach that enhances the separation of peptides for sequencing by mass spectrometry analysis.We here adapt a mathematical model from ecology, namely, the capture-recapture model with a closed population and time-varying and heterogeneous individual probabilities of capture, to model the number of peptide identifications across the various cycles of a typical MudPIT experiment. In the absence of any prior information on abundance levels, the model can be used to estimate the total number of proteins in the experimental sample. We apply the model to a recent MudPIT-based experiment to estimate the total number of rat lung endothelial cell surface proteins. The model provides some practical guidelines for planning MudPIT experiments.

Animals↗

PubMed2006

Metal affinity capture tandem mass spectrometry for the selective detection of phosphopeptides.

We report a new method called metal affinity capture that when coupled with tandem mass spectrometry (MAC-MSMS) allows for the selective detection and identification of phosphopeptides in complex mixtures. Phosphopeptides are captured as ternary complexes with Ga(III) or Fe(III) and N(alpha),N(alpha)-bis(carboxymethyl)lysine (LysNTA) in solution and electrosprayed as doubly or triply charged positive ions. The gas-phase complexes uniformly dissociate to produce a common (LysNTA + H)+ ion that is used as a specific marker in precursor ion scans. The advantages of MAC-MSMS over the current methods of phosphopeptide detection are as follows. (1) MAC-MSMS uses metal complexes that self-assemble in solution at pH <5, which is favorable for the production of positive ions by electrospray. (2) Phosphorylation at tyrosine, serine, and threonine is detected by MAC-MSMS. (3) The phosphopeptide peaks in the mass spectra are encoded with the 69Ga-71Ga isotope pattern for selective recognition in mixtures. Detection by MAC-MSMS of singly and multiply phosphorylated peptides in tryptic digests is demonstrated at low-nanomolar protein concentrations.

Amino Acid Sequence↗

PubMed2006

Strategy for the identification of sites of phosphorylation in proteins: neutral loss triggered electron capture dissociation.

We have previously demonstrated the suitability of data-dependent electron capture dissociation (ECD) for incorporation into proteomic strategies. The ability to directly determine sites of phosphorylation is a major advantage of electron capture dissociation; however, the low stoichiometry associated with phosphorylation means that phosphopeptides are often overlooked in data-dependent ECD analyses. In contrast, collision-induced dissociation (CID) tends to result in loss of the labile phosphate group, often at the expense of sequence fragments. Here, we demonstrate a novel strategy for the characterization of phosphoproteins which exploits the neutral loss feature of CID such that focused ECD of phosphopeptides is achieved. Peptides eluting from a liquid chromatograph are first subjected to CID, and if a neutral loss of 98 Da (corresponding to H3PO4) from the precursor is observed, ECD of that same precursor is performed; i.e., the method comprises neutral loss triggered ECD (NL-ECD-MS/MS). The method was applied to tryptic digests of beta-casein and alpha-casein. For alpha-casein, four sites of phosphorylation were identified with NL-ECD-MS/MS compared with a single site identified by ECD-MS/MS. The method also resulted in ECD of a doubly phosphorylated peptide. A further benefit of the method is that overall protein sequence coverage is improved. Sequence information from nonphosphorylated peptides is obtained as a result of the CID step.

Amino Acid Sequence↗

PubMed1999

Lectin-based affinity capture for MALDI-MS analysis of bacteria.

Immobilized lectins have now been incorporated into affinity surfaces that can be used to isolate broad classes of samples for mass spectrometric analysis. A carbohydrate and a bacterial species that displays the carbohydrate binding motif were isolated and concentrated out of solutions containing salt, urea, buffers, and other contaminants that are deleterious to MALDI mass spectrometry. Concanavalin A was immobilized to a gold foil via a self-assembled monolayer. Samples in phosphate buffer or urine were applied to the capture surface and allowed to interact. The capture surface was then washed to remove salts and other unbound components and subjected to matrix-assisted laser desorption/ionization on a time-of-flight mass spectrometer. The lectin-derivatized surface allowed samples to be concentrated and readily characterized at relatively low levels.

Bacteria↗

PubMed2000

A Salmonella detection system using an engineered DNA binding protein that specifically captured a DNA sequence.

We have developed a novel method for the detection with high selectivity of a double-stranded DNA fragment using an engineered DNA-binding protein, DnaA IV, a fusion protein of the DNA-binding domain of DnaA and glutathione S-transferase. The DNA fragment detection system is based on DNA-protein interaction and consists of sequence-specific binding of DnaA IV with a DNA fragment containing the DnaA box. DnaA IV, while not capturing other DNA fragments, specifically captured that containing the DnaA box. Because the oriC fragment containing the DnaA box could be specifically amplified by PCR from the genus Salmonella, the DNA fragment detection system was adapted for the detection of Salmonella. The Salmonella detection system using PCR amplification and the engineered DNA-binding protein could distinguish 104 cfu/mL Salmonella from 106 cfu/ mL contaminating bacteria.

Culture Media↗

PubMedDate not supplied

Windows-based guided data capture software for mass-scale thermophysical and thermochemical property data collection.

Guided data capture software (GDC) is described for mass-scale abstraction from the literature of experimental thermophysical and thermochemical property data for organic chemical systems involving one, two, and three components, chemical reactions, and chemical equilibria. Property values are captured with a strictly hierarchical system based upon rigorous application of the thermodynamic constraints of the Gibbs phase rule with full traceability to source documents. Key features of the program and its adherence to scientific principles are described with particular emphasis on data-quality issues, both in terms of data accuracy and database integrity.

Journal Article↗