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At least 793 records · Page 44Linked to original sources

PubMed2002

Isolating vessels from the mouse brain for gene expression analysis using laser capture microdissection.

Studies of gene expression often examine a pool of RNA extracted from the diverse cell types making up a tissue. We have developed a method for isolating vessels from the brain in order to understand the changes occurring in the vessels during the pathogenesis of cerebral malaria. Vessels were visualised by incubating sections of mouse brain with a substrate for alkaline phosphatase. Vessels were collected by laser capture microdissection and the specificity was monitored by measuring the expression of cell-specific markers. RNA from the captured vessels was highly enriched in mRNA for genes associated with endothelial cells and pericytes. Measurement of indoleamine 2,3-dioxygenase mRNA indicated it was possible to detect changes in gene expression, due to malaria infection, occurring specifically within the vessels. Laser capture microdissection can be used to study changes in gene expression occurring at the blood-brain barrier.

Alkaline Phosphatase↗

PubMed1999

Comparison of the Murex Hybrid Capture CMV DNA (v2.0) assay and the pp65 CMV antigenemia test for the detection and quantitation of CMV in blood samples from immunocompromised patients.

BACKGROUND: Presently the semiquantitative pp65 cytomegalovirus (CMV) antigenemia test on white blood cells is often used for monitoring transplant patients for the appearance of active CMV infections. However, the need for immediate processing of the specimens and the lack of interlaboratory standardization of the test may sometimes be a disadvantage. OBJECTIVE: The aim of this study was to investigate the value of the recently developed second version of the Murex Hybrid Capture (MHC) CMV-DNA assay (v 2.0) in comparison with the CMV-pp65 test. The MHC CMV-DNA assay is a quantitative solution hybridization antibody capture assay, using alkaline phosphatase conjugated antibodies and a chemiluminescent substrate. STUDY DESIGN: 248 EDTA blood samples from 33 renal transplant patients and 32 samples from 22 other immunocompromised patients were tested by both the MHC CMV-DNA assay and the CMV-pp65 test. RESULTS: The qualitative ( + or -) results of both tests showed an overall concordance of 81.4%. Calculations on the basis of discordancy analyses showed that the sensitivity, the specificity, and the positive and negative predictive values were 87.7, 98.3, 98.6, 85.2% for the MHC CMV-DNA assay and 76.6, 100, 100, 75.5% for the CMV-pp65 test. Comparison of the quantitative results of both tests systems showed a correlation coefficient of 0.837. In addition, retesting of 50 samples with the MHC-CMV-DNA assay showed an excellent reproducibility with a correlation coefficient of 0.992. All patients which were tested regularly (at least five samples) became either positive with both tests or with none of them. Neither test system detected CMV significantly earlier than the other one. Both tests became strongly positive in all transplant patients with symptomatic CMV infections, and both tests showed a rapid decline of CMV during subsequent antiviral treatment. CONCLUSION: The quantitative Murex Hybrid Capture CMV-DNA assay (v 2.0) may become a valuable additional tool in CMV diagnosis. Further studies will be needed to support this preliminary judgement.

AIDS-Related Opportunistic Infections↗

PubMed2003

A shallow parser based on closed-class words to capture relations in biomedical text.

Natural language processing for biomedical text currently focuses mostly on entity and relation extraction. These entities and relations are usually pre-specified entities, e.g., proteins, and pre-specified relations, e.g., inhibit relations. A shallow parser that captures the relations between noun phrases automatically from free text has been developed and evaluated. It uses heuristics and a noun phraser to capture entities of interest in the text. Cascaded finite state automata structure the relations between individual entities. The automata are based on closed-class English words and model generic relations not limited to specific words. The parser also recognizes coordinating conjunctions and captures negation in text, a feature usually ignored by others. Three cancer researchers evaluated 330 relations extracted from 26 abstracts of interest to them. There were 296 relations correctly extracted from the abstracts resulting in 90% precision of the relations and an average of 11 correct relations per abstract.

Abstracting and Indexing↗

PubMed1986

Capture-ELISA for serum IgM antibody to respiratory syncytial virus.

A four-component solid-phase capture enzyme immunoassay was set up to test for serum IgM antibody to respiratory syncytial (RS) virus and was compared with immunofluorescence assay (IFA). A total of 128 young children with acute respiratory infections were studied. Thirty-six were shown to be RS virus-positive by the detection of RS virus in nasopharyngeal secretions and 92 were RS virus-negative. A serum specimen was collected after admission to the hospital (days 0-4) and a further specimen was obtained during days 10-14. Out of 36 RS virus-positive patients, 28 (77.7%) were found to be positive for IgM by both capture-ELISA and IFA. Out of 92 RS virus-negative patients 5 (5.4%) were IgM-positive. Four false-positive results were obtained by IFA due to the presence of rheumatoid factor. The capture-ELISA was shown to be a reliable technique in detecting specific IgM antibody to RS virus.

Antibodies, Viral↗

PubMed1988

The development and evaluation of a mu-capture ELISA detecting Chlamydia-specific IgM.

A mu-capture enzyme-linked immunosorbent assay (ELISA) for detecting chlamydia-specific IgM was developed by use of the heat stable, lipopolysaccharide group-specific antigen and an alkaline phosphatase-labelled anti-chlamydia group-specific monoclonal antibody conjugate. The test was used to study the serological response in chlamydial respiratory tract infection among patients with acute respiratory tract symptoms in Cambridgeshire during the past 7 years. Results were compared with those of the complement fixation test (CFT) in routine use as well as those of a whole inclusion indirect immunofluorescence (WIF) test for IgM. Correlation between results of the mu-capture ELISA and those of the WIF test was 87.5%. The percentage of patients in whom specific IgM was found fell with increasing age. This may be due to lack of recall of IgM as a response to reinfection. Chlamydia-specific IgM was more likely to be detected when the CFT titre was greater than or equal to 64 and was rarely detected more than 6 months after the onset of symptoms. However, several patients less than 20 years of age were found to have specific IgM with CF antibody titres less than 64. We have found the mu-capture ELISA a useful test for the diagnosis of respiratory tract chlamydial infections, particularly in younger patients.

Adolescent↗

PubMed2006

Capture-recapture analysis to estimate the incidence of invasive meningococcal disease in Germany, 2003.

The incidence of invasive meningococcal disease (IMD) in Germany in 2003 was estimated by the two-source capture-recapture method. As a unique personal identifier was unavailable, cases with IMD tested at the National Reference Centre for Meningococci (NRZM) were matched with cases reported to the Robert Koch Institute (RKI) through the statutory surveillance system by using demographic and disease-specific variables common to both datasets. The estimated overall incidence was 1.1 IMD cases/100,000 inhabitants, with a sensitivity of ascertainment of 64.8% for NRZM and 89.4% for RKI. Case-fatality rate was estimated at 8.8%. Adjustment for heterogeneity of capture according to age, region and serogroup observed in the NRZM (but not RKI) source had minimal effect on the estimated incidence. The IMD incidence estimated by capture-recapture analysis is thus only slightly higher than through statutory surveillance data. As a degree of positive dependence between the systems cannot be ruled out, this estimate may still be an underestimate. However, under ascertainment appears insufficient to explain the low incidence of IMD in Germany compared to other European countries.

Adolescent↗

PubMed2001

Lectin and carbohydrate affinity capture surfaces for mass spectrometric analysis of microorganisms.

In a preliminary report (Bundy, J. L.; Fenselau, C. Anal. Chem 1999, 71, 1460-1463), we demonstrated the use of lectin-derivatized surfaces to capture and concentrate complex carbohydrates as well as microorganisms from sample matrixes unamenable to direct MALDI mass spectrometry. Here, we extend the work to include samples representative of a wider variety of microorganisms of importance to human health and of enveloped viruses. In this study, lectins were immobilized directly to a membrane surface via primary amines. A complementary approach was also explored, using immobilized carbohydrates to capture bacteria via microbial lectins expressed on their surfaces. The carbohydrate-based surfaces were constructed by first immobilizing streptavidin to the membrane, followed by attachment of a commercially produced biotin/carbohydrate polymer. Acid treatment of the sample prior to mass spectrometric analysis permits the observation of protein biomarkers from the captured microbial samples in the 5-20 kDa mass range. Bacteria samples were detected from physiological buffers, urine, milk, and processed chicken samples using the biocapture probes. Viral samples were detected from culture based on glycoprotein moieties desorbed directly from the surface. The carbohydrate-based system provided greater sensitivity than the lectin system, possibly due to the larger number of accessible saccharide ligands on the polymer.

Carbohydrates↗

PubMed2002

Mass spectrometry after capture and small-volume elution of analyte from a surface plasmon resonance biosensor.

The identification of binding partners of proteins by mass spectrometry following specific capture on a biosensor surface is a promising tool for proteomics research and the identification and characterization of protein-protein interactions. Previous approaches include the direct ionization of analyte from the biosensor chip on a matrix assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOFMS) apparatus and the on-chip digestion followed by elution, chromatographic concentration of the fragments, and electrospray mass spectrometry. In the present paper, using the small-volume microfluidic sample manipulation technique with oscillatory flow reported recently (Abrantes et al. Anal. Chem. 2001, 73, 2828-2835), analyte is shown to be eluted from the sensor surface into a small volume of buffer that promotes dissociation from the capture surface and delivery to the mass spectrometer. Both the incubation of the sensor surface with the sample and the recovery of analyte can be achieved with a few microliters and conducted until steady-state is attained. Because the procedure is non-destructive for the sensor surface, multiple cycles of capture and elution allow the transfer and concentration of analyte into the elution buffer. The eluted analyte can be studied directly by MALDI-TOFMS, or subjected to proteolytic digestion for protein identification. Transfer into the elution buffer and MALDI-TOFMS detection was achieved from 5 microL of starting samples containing <50 fmol of analyte. Examples are presented for the specific detection and recovery of a protein from a complex mixture of cytosolic proteins.

Animals↗

PubMed2004

A gas chromatograph/resonant electron capture-TOF mass spectrometer for four dimensions of negative ion analytical information.

A prototype gas chromatograph (GC) electron monochromator (EM) reflectron time-of-flight (TOF) mass spectrometer has been constructed and demonstrated to simultaneously record four-dimensional resonant electron capture (REC) mass spectra (m/z, ion-intensity, electron-energy, and retention time) of electron-capturing compounds in real time. Specifically, complete REC mass spectra of all of the components in a mixture of perfluorocarboxylic acids and in a sample of pentafluorobenzyl alcohol were recorded in the GC mode. For each compound, the data enable one to distinguish different electronic states of the molecular ion and different possible decomposition pathways for each state. This new instrument can be used to obtain analytical information unrecognizable by any other mass spectrometric technique from the isomeric species of a variety of electron-capturing structures.

Benzyl Alcohols↗

PubMed2005

Radio frequency plasma polymer coatings for affinity capture MALDI mass spectrometry.

Surface modification of MALDI probes is an attractive approach for combining bioaffinity isolation of targeted biomolecules with mass spectrometric analysis of the captured species. In this work, we demonstrate that a polymer thin film, produced by pulsed rf plasma polymerization of allylamine and deposited directly on a MALDI probe, can be subsequently biotinylated to develop a bioaffinity capture MALDI probe. The synthesis and characterization of the probe by XPS, FT-IR, and AFM is described, and the selective isolation of avidin from a three-component mixture of avidin, lysozyme, and cytochrome c is presented. These initial results offer encouragement for the further exploration of rf plasma polymer deposition as a novel approach for the development of on-probe affinity capture MALDI probes.

Biotinylation↗

PubMed2004

Photoimmobilization of proteins for affinity capture combined with MALDI TOF MS analysis.

Affinity capture surfaces can be prepared in a number of ways. A method of obtaining such surfaces through UV-activated immobilization of binding proteins using a benzophenone derivative is reported. Photoimmobilized protein G was used to selectively capture and preconcentrate bovine IgG from a mixture with BSA, and the affinity of photoattached concanavalin A toward ovalbumin was compared with that of commercially available concanavalin A on agarose beads. The results of the capture after tryptic digestion were analyzed by MALDI TOF MS. Immobilized trypsin was also prepared through photoimmobilization and later used to digest hemoglobin. Immobilized enzyme digestion resulted in more partial cleavages than solution-phase digestion. More methionine and tryptophan oxidation was also observed. Photoimmobilization was shown to be a quick and easy way of immobilizing ligands on surfaces.

Amino Acid Sequence↗

PubMed2000

Laser-induced electron capture mass spectrometry

Two techniques are reported for detection of electrophorederivatized compounds by laser-induced electron capture time-of-flight mass spectrometry (LI-EC-TOF-MS). In both cases, a nitrogen laser is used to induce the electron capture. The analyte is deposited in a matrix consisting of a compound with a low ionization potential such as benzo[ghi]perylene in the first technique, where the electron for electron capture apparently comes from this matrix. In the second technique, the analyte is deposited on a silver surface in the absence of matrix. It seems that "monoenergetic" ions instantly desorb from the target surface in the latter case, since the peak width in the continuous extraction mode essentially matches the pulse width of the laser (4 ns). Ten picomoles of 3-O-(pentafluorobenzyl)-alpha-estradiol were detected at a S/N > or = 50, where the spot size of the laser was approximately 0.25% of the sample spot. It is attractive that simple conditions can enable sensitive detection of electrophores on routine TOF-MS equipment. The technique can be anticipated to broaden the range of analytes in both polarity and size that can be detected by EC-MS relative to the range for GC/EC-MS.

Journal Article↗

PubMed1994

Photoaffinity labeling of cytochrome P450 2B4: capture of active site heme ligands by a photocarbene.

Spiro[adamantane-2,2'-diazirine], which produces adamantyl carbene upon photolysis, binds tightly to P450 2B4 (KS = 3.2 microM), giving a normal substrate binding difference spectrum. Irradiation of 2-[3H]adamantane diazirine at 365 nm in the presence of native, ferric P450 2B4 resulted in first-order photolysis (t1/2 = 1.8 min). The main product was 2-[3H]adamantanol, with about 6% of the radioactivity covalently bound to P450 2B4. With the ferrous carbonyl form of P450 2B4, 2-adamantanol production decreased and protein labeling increased to 12%. When ferric cyanide 2B4 was used, 2-adamantanecarbonitrile was formed in addition to 2-adamantanol. The nitrile appears to have resulted from capture of the iron-bound cyanide ligand by the carbene. The use of multiple cycles of photolysis increased the percentage of protein labeling to 76%. Photolabeling was inhibited by known 2B4 substrates and inhibitors. Also, N-demethylation of benzphetamine and generation of a substrate binding difference spectrum by benzphetamine were both inhibited stoichiometrically with the fraction of radiolabeled protein. The labeled protein was permanently converted to the high-spin state, as indicated by the characteristic change in the absorbance spectrum, demonstrating irreversible occupation of the substrate binding site by the adamantyl residue. Mild acid hydrolysis of radiolabeled 2B4 at the five Asp-Pro bonds generated a 2-kDa peptide which carried 78% of the radioactivity. These results are interpreted as the result of the active site carbene reacting by three competing pathways: capture of the heme sixth ligand to yield either 2-adamantanol or 2-adamantanecarbonitrile, capture of an unbound active site water molecule to yield adamantanol, and covalent attachment to a protein residue. Thus, the P450 2B4 active site appears to contain at least one unbound water molecule in addition to the heme aquo sixth ligand, even when substrate is present.

Adamantane↗

PubMedDate not supplied

Quantitative screening of yeast surface-displayed polypeptide libraries by magnetic bead capture.

Magnetic bead capture is demonstrated here to be a feasible alternative for quantitative screening of favorable mutants from a cell-displayed polypeptide library. Flow cytometric sorting with fluorescent probes has been employed previously for high throughput screening for either novel binders or improved mutants. However, many laboratories do not have ready access to this technology as a result of the limited availability and high cost of cytometers, restricting the use of cell-displayed libraries. Using streptavidin-coated magnetic beads and biotinylated ligands, an alternative approach to cell-based library screening for improved mutants was developed. Magnetic bead capture probability of labeled cells is shown to be closely correlated with the surface ligand density. A single-pass enrichment ratio of 9400 +/- 1800-fold, at the expense of 85 +/- 6% binder losses, is achieved from screening a library that contains one antibody-displaying cell (binder) in 1.1 x 10(5) nondisplaying cells. Additionally, kinetic screening for an initial high affinity to low affinity (7.7-fold lower) mutant ratio of 1:95,000, the magnetic bead capture method attains a single-pass enrichment ratio of 600 +/- 200-fold with a 75 +/- 24% probability of loss for the higher affinity mutant. The observed high loss probabilities can be straightforwardly compensated for by library oversampling, given the inherently parallel nature of the screen. Overall, these results demonstrate that magnetic beads are capable of quantitatively screening for novel binders and improved mutants. The described methods are directly analogous to procedures in common use for phage display and should lower the barriers to entry for use of cell surface display libraries.

Antibodies↗

PubMedDate not supplied

Resin-capture and release strategy toward combinatorial libraries of 2,6,9-substituted purines.

A resin-capture and release strategy for making combinatorial 2,6,9-trisubstituted purine libraries is demonstrated by capturing N9-derivatized purines at the C6 position with a thio-modified polymer. The C2 fluoro group is subsequently substituted with primary and secondary amines followed by thioether oxidation and release by C6 substitution with amines and anilines. This approach complements a previously reported strategy where a 6-phenylsulfenylpurine scaffold was captured at the C2 position with a resin-bound amine.(3)

Combinatorial Chemistry Techniques↗

PubMed2003

Electron capture dissociation initiates a free radical reaction cascade.

For small cyclic peptides, one electron capture by the [M + 2H](2+) ion generates numerous fragments corresponding to amino acid losses, side-chain losses, and losses of some low molecular weight species such as H(2)O, CH(3)(*), C(3)H(6), and (*)CONH(2). As predicted, the side-chain cleavages are amplified relative to linear peptides of similar size, but the amino acid losses were unexpected because they require that one electron capture cause more than one backbone cleavage, a phenomenon which necessitates further refinement or reinterpretation of current ECD mechanisms. A modified mechanism is postulated in which nonergodic electron capture fragmentation generates an alpha-carbon radical species that then propagates along the protein backbone. This radical migration initiates multiple free radical rearrangements, which cause both multiple backbone cleavages and additional side-chain cleavages.

Amino Acid Sequence↗

PubMed2006

Insulin capture by an insulin-linked polymorphic region G-quadruplex DNA oligonucleotide.

Insulin capture by a G-quadruplex DNA oligonucleotide containing a two-repeat sequence of the insulin-linked polymorphic region (ILPR) of the human insulin gene promoter region is reported. The immobilized oligonucleotide was demonstrated to capture human insulin from standard solutions and from nuclear extracts of pancreatic cells with high selectivity, using affinity MALDI mass spectrometry and affinity capillary chromatography. Insulin was preferentially captured by the two-repeat ILPR oligonucleotide over another G-quadruplex-forming oligonucleotide, the thrombin-binding aptamer, as well as over a single repeat of the ILPR sequence that is not capable of forming the G-quadruplex architecture. Binding was shown to involve the beta chain of insulin. The discovery raises the possibility that insulin may bind to G-quadruplex DNA formed in the ILPR in vivo and thereby play a role in modulation of insulin gene expression, and it provides a basis for design of insulin analogues to probe this hypothesis. The availability of a DNA ligand to human insulin has analytical importance as well, offering an alternative to antibodies for in vitro or in vivo detection and sensing of insulin as well as its isolation and purification from biological samples.

Aptamers, Nucleotide↗

PubMed2001

Mercaptan-capturing properties of mushrooms.

Mercaptan-capturing properties of 33 kinds of mushrooms were measured. The mushrooms having a high capturing ability toward methyl mercaptan (MeSH) were Agaricus bisporus, A. campestris, Boletus fraternus, B. subvelutipes, Gyrodon lividus, Leccinum scabrum, Suillus grevillei, Morchella esculenta, Russula nigricans, Hypholoma sublateritium, and Lyophyllum sykosporum. These are liable to change their color when injured. The mixture of their acetone powders, which contain polyphenol oxidases, and phenolic compounds such as tyrosine, gamma-L-glutaminyl-4-hydroxybenzene (GHB), DOPA, variegatic acid, grevillin B and C, and pigments, and fluorescent compounds from H. sublateritium also showed high MeSH-capturing properties. 2,5-Bis(methylthio)-DOPA was isolated from the reaction mixture of tyrosine and MeSH with tyrosinase, and the existence of 2- and 5-methylthio-DOPAs was also suggested. Furthermore, acetone powders from fruits and vegetables oxidized the above diphenolic compounds to bind MeSH.

Agaricales↗