Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data fragmentation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
PubMedDate not supplied

[Correlation of fragmented cells with lytic products and other hematologic data].

In a group of 38 children under three months of age, the FRBC, split products of fibrinogen, red blood cells per microliter, hematocrit and mean corpuscular volume were determined, trying to establish a correlation between the first parameter and the other. Only a significant correlation with the mean corpuscular volume was found. Most of the cases with more than three percent of FRBC had a diagnosis of severe infection. The same phenomenon was observed in the group of more than 8 microgram/ml of FSP, but there was no association between both groups. We suggest an etiology related with fasting and nonrelated with disseminated intravascular coagulation for microangiopathic hemolysis in the newborn with infection.

Bacterial Infections↗
PubMed1991

Population genetic data determined for five different single locus minisatellite probes.

We report on the population genetic data (frequencies of restriction fragments, heterozygosity rates, and mutation rates) obtained by analysis of approximately 1100 Hinfl-digested DNAs from West Germans. Probe G3 detects a common 1.7 kb DNA fragment showing a population frequency of about 13%. All the other fragments detected with probes MS1, MS31, MS43, G3 and YNH24 show frequencies of less than 8%. These data suggest that single locus DNA probes can provide valuable information for parentage evaluation and individualization.

DNA Probes↗
PubMed2001

Identification of caspase-3 and caspase-activated deoxyribonuclease in rat blastocysts and their implication in the induction of chromatin degradation (but not nuclear fragmentation) by high glucose.

Previous investigations have shown that maternal diabetes impairs rodent embryo development during the earliest phase of gestation. Exposure to high concentrations of glucose before implantation results in a decrease in the number of cells per embryo and in a concomitant increase in two nuclear markers of apoptosis, chromatin degradation and nuclear fragmentation. In the present study, we show that two intracellular effectors of apoptosis, caspase-3 and caspase-activated deoxyribonuclease (CAD), are involved in the embryotoxicity of high glucose. Using reverse transcription-polymerase chain reaction and immunocytochemistry, we first demonstrated that these two effectors were expressed in rat blastocysts. The two effectors were detected in all the cells of the blastocysts and the immuno-signals were excluded from the nuclei. Rat blastocysts were incubated for 24 h in either 6 mM or 28 mM glucose in the presence or absence of specific inhibitors (DEVD-CHO [10 microM] against caspase-3 and aurin [1 microM] against CAD). After incubation, blastocysts were examined for the proportion of nuclei showing signs of chromatin degradation or nuclear fragmentation. Addition of DEVD-CHO or aurin was found to inhibit the increase in chromatin degradation induced by high glucose. None of these two inhibitors prevented the increase in nuclear fragmentation triggered by excess glucose. Our data indicate that chromatin degradation and nuclear fragmentation are two nuclear damages that are induced separately by high glucose in rat blastocysts. Chromatin degradation is apparently mediated by the activation of caspase-3 and CAD.

Animals↗
PubMed1998

Interaction between SecA and SecYEG in micellar solution and formation of the membrane-inserted state.

Preprotein translocation in Escherichia coli is mediated by the translocase with SecA as peripheral ATPase and SecY, SecE, and SecG as membrane domain. To facilitate large-scale purification of the SecYEG heterotrimer, SecY was fused at its amino terminus with a hexahistidine tag and co-overexpressed with SecE and SecG. The presence of the His tag allowed purification of homogeneously pure SecYEG complex by a single anion-exchange chromatographic step starting from octyl glucoside-solubilized inner membranes. Endogenous levels of SecD and SecF copurified with the SecYEG protein. Purified SecYEG complex retained a nativelike, alpha-helical conformation in octyl glucoside and in micellar solution binds SecA with high affinity. In the presence of the nonhydrolyzable nucleotide analogue adenosine 5'-(beta, gamma-imidotriphosphate), octyl glucoside-solubilized SecYEG is nearly as effective as the reconstituted enzyme in inducing the formation of a proteinase K-protected 30 kDa fragment of 125I-labeled SecA, while SecYEG is proteolyzed to fragments smaller than 6 kDa. These data demonstrate that the 30-kDa SecA fragment is not protected by the lipid phase nor by SecYEG but rather indicate that it represents a SecYEG- and nucleotide-induced stable conformational state of a SecA domain.

Adenosine Triphosphatases↗
PubMed2004

Extraribosomal cyclic tetradepsipeptides beauverolides: profiling and modeling the fragmentation pathways.

Profiling of cyclic tetradepsipeptides beauverolides was tested as a chemotaxonomic tool for fungal strain identification/discrimination. Two new tetradepsipeptides, beauverolides Q and R, were characterized by tandem mass spectrometry. Specific elimination of 113 atomic mass units from both protonated and sodiated molecules of beauverolides is ubiquitous for all 12 most dominant congeners evaluated in this profiling study. Reconstruction of the total ion chromatogram, according to this neutral fragment release, was used for data filtering and selectivity enhancement. Selective ring opening and fragment ion formation of beauverolide I are discussed in detail utilizing high-level theoretical modeling of the fragmentation pathways.

Biomarkers↗
PubMed2003

Microarray of recombinant antibodies using a streptavidin sensor surface self-assembled onto a gold layer.

We have developed a sensitive method for the detection of recombinant antibody-antigen interactions in a microarray format. The biochip sensor platform used in this study is based on an oriented streptavidin monolayer that provides a biological interface with well-defined surface architecture that dramatically reduces nonspecific binding interactions. All the antibody or antigen probes were biotinylated and coupled onto streptavidin-coated biochip surfaces (1 microL total volume). The detection limits for the immobilized probes on the microarray surface were 0.5 microgram/mL (200 fmol/spot) for the peptide antigen and 0.1 microgram/mL (3 fmol/spot) for the recombinant antibodies. Optimal concentrations for the detection of the Cy5-labeled protein target were in the range of 20 micrograms/mL. Protein microchips were used to measure antibody-antigen kinetics, to find optimal temperature conditions, and to establish the shelf life of recombinant antibodies immobilized on the streptavidin surface. For recombinant antibody fragments with a kDa of 10-100 nM, we have established an easy and direct immunoassay. In addition, we developed an indirect method for antibody detection with no need for expensive and time-consuming antibody purifications and modifications. Such a method was shown to be useful for large-scale screening of recombinant antibody fragments directly after their functional expression in bacteria. Our data demonstrate that recombinant antibody fragments are suitable components in the construction of antibody chips.

Antibodies↗
PubMed2004

Using molecular sizes of simple sequence repeats vs. discrete binned data in assessing probability of ancestry: application to maize hybrids.

Most inferential methods for profiling genotypes based upon the use of DNA fragments use molecular-size data transcribed into discrete bins, which are intervals of DNA fragment sizes. Categorizing into bins is labor intensive with inevitable arbitrariness that may vary between laboratories. We describe and evaluate an algorithm for determining probabilities of parentage based on raw molecular-size data without establishing bins. We determine the standard deviation of DNA fragment size and assess the association of standard deviation with fragment size. We consider a pool of potential ancestors for an index line that is a hybrid with unknown pedigree. We evaluate the identification of inbred parents of maize hybrids with simple sequence repeat data in the form of actual molecular sizes received from two laboratories. We find the standard deviation to be essentially constant over the molecular weight. We compare these results with those of parallel analyses based on these same data that had been transcribed into discrete bins by the respective laboratories. The conclusions were quite similar in the two cases, with excellent performance using either binned or molecular-size data. We demonstrate the algorithm's utility and robustness through simulations of levels of missing and misscored molecular-size data.

Algorithms↗
PubMed1981

[Determination of glucoamylase activity using an enzyme electrode].

Both, the differing definitions of glucoamylase activity and the different determination of the fragment, glucose, preclude a comparison of literature data. Specific enzymatic determination of the fragment, glucose, with an enzyme electrode is proposed. The contribution describes the manufacture of an enzyme electrode from a commercial pO2-electrode and immobilized GOD. The measurement may be carried out by kinetic determination of utilized oxygen or oxygen peroxide formed. The continuous measurement proposed for serial experiments is made via a calibration curve, whose regression coefficient was determined to be 0.999. Depending on the enzyme activity, the reaction time is between 15 s and 3 min.

Electrodes↗
PubMed1976

Comparison of the physicochemical properties of fragment D derivatives of fibrinogen and fragment D-D of cross-linked fibrin.

The molecular weight of Fragment D derivatives obtained from plasmic digests of fibrinogen and cross-linked fibrin was determined by equilibrium sedimentation and compared with the summated molecular weight of their polypeptide chains observed after electrophoresis of reduced protein in sodium dodecyl sulfate polyacrylamide gels. The measured molecular weight of Fragment D (Stage 2) of fibrinogen is 103 500, which is compatible with a molecule containing only one each of the Aalpha (13 000), Bbeta (43 000) and gamma (39 000) chain remnants. Fragment D-D of cross-linked fibrin has a molecular weight of 189 000, compatible with a molecule containing one isopeptide-bound gamma-gamma chain (80 000) and two each of Bbeta (43 000) and Aalpha (13 000) chain remnants. The NH2-terminal amino acid residues of the Fragment D derivatives were measured quantitatively using a thioacetic-thioglycolic acid method, and molar quantities were calculated on the basis of the molecular weights determined by equilibrium sedimentation. Fragment D preparations obtained from Stage 2 and Stage 3 digests of fibrinogen have 3 mol of NH2-terminal amino acids per molecule, while Fragment D-D has seven. These data support the view that two Fragment D molecules, each of three polypeptide chains, are derived by plasmic degradation from each fibrinogen molecule, and that an isopeptide-bound, six chain Fragment D-D molecule is released from cross-linked fibrin by plasmin. Equlibrium sedimentation measurement of the molecular weights of Fragment X (Stage 1 and Stage 2) and Fragment Y are 265 000 and 148 000, respectively. These values are compatible with asymmetric cleavages of Fragment X to Fragments Y and D (Stage 2), and of Fragment Y to Fragments D (Stage 2) and E, and with a fibrinogen model in which the two halves are joined by disulfide bonds only in the amino-terminal regions.

Electrophoresis, Polyacrylamide Gel↗
PubMed1983

Preliminary crystallographic study of the Fab fragment of a monoclonal anti-phenylarsonate antibody.

Preliminary crystallographic data are given for the Fab fragment of a monoclonal anti-p-phenylarsonate antibody. This crystalline Fab fragment was found by screening a number of monoclonal anti-arsonate antibodies obtained from hybrids of A/J immune spleen cells with a non-secreting mouse myeloma line. The protein crystallizes in the monoclinic space group P21 with a = 86.2 +/- 0.1 A, b = 80.4 +/- 0.2 A, c = 75.8 +/- 0.1 A, beta = 90.3 +/- 0.1 degrees. Precession photographs show X-ray reflections extending to a resolution of 3 A.

Antibodies, Monoclonal↗
PubMed2005

Fragmentation of peptides in MALDI in-source decay mediated by hydrogen radicals.

In-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) shares some similarities with the novel fragmentation technique electron capture dissociation (ECD). In both reactions, the otherwise strong N-C(alpha) bond is cleaved, forming fragment ions of the c and z types, while labile posttranslational modifications are preserved. Therefore, it is tempting to assume that ISD and ECD have some mechanistic aspects in common. Because electrons are present in the MALDI plume, we investigated the previously suggested possibility that ISD is a variation of ECD. However, experiments with peptides with only one site for efficient protonation revealed that ISD is not caused by electron capture. Instead, ICD seems to be induced by hydrogen atoms generated by a photochemical reaction of the matrix. We provide evidence for this reaction by hydrogen/deuterium exchange experiments with peptides containing a minimal number of exchangeable hydrogen atoms. The hydrogen atom model in ECD is indirectly supported by the proposed fragmentation mechanism for ISD, because our data suggest that hydrogen radicals can induce fragmentation by cleavage of the N-C(alpha) bond, independent from their origin.

Electrons↗
PubMed1994

Preliminary study of the metabolism of 17 alpha-methyltestosterone in horses utilizing gas chromatography-mass spectrometric techniques.

Little is known about the metabolism of 17 alpha-alkyl anabolic steroids in horses. In this study, the metabolism of 17 alpha-methyltestosterone is investigated by oral administration of a (1 + 1) mixture of the steroid and its deuteriated analogue. Both compounds were synthesized from dehydroisoandrosterone (DHA), using a Grignard reaction followed by an Oppenauer oxidation. Post-administration urine extracts were analysed by gas chromatography--mass spectrometry (GC-MS) using both electron impact (IE) and chemical ionization (CI). Interpretation of the data was facilitated by observation of the fragment ions present in the mass spectra. Notably, the D-ring fragment ions were indicative of 15- or 16-hydroxylation, where 16-hydroxy metabolites showed ion pairs at m/z 218/221 and at m/z 231/234 while 15-hydroxy compounds gave the 231/234 ion pair alone. Unaltered D-rings showed fragment ions at m/z 143/146. The data showed that the main phase 1 metabolic processes were partial and complete reduction of the 3-oxo-4-ene group, 15-hydroxylation, 16-hydroxylation, 17-epimerization and hydroxylation at at least two other undetermined sites, postulated as the 6 and 11 positions. Phase 2 metabolism, in the form of glucuronide and sulfate formation, was also common. The information provided by this investigation will result in improved effectiveness of confirmatory analytical procedures for 17 alpha-alkyl anabolic steroids.

Administration, Oral↗
PubMed1989

Image analysis of restriction enzyme fingerprint autoradiograms.

A genome mapping system has been developed that reads and assembles data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. Input data for the system can be most effectively obtained by the use of a scanning densitometer and image-processing package, such as that described in this article. The image-processing procedure involves preliminary location of bands, cooperative tracking of lanes by correlation of adjacent bands, a precise densitometric pass, alignment of the marker bands with the standard, optional interactive editing, and normalization of the accepted bands.

Animals↗
PubMed1999

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry for monitoring alkylation of beta-lactoglobulin B exposed to a series of N-substituted acrylamide monomers.

Delayed-extraction matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry, in both linear and reflectron modes, has been used to examine the alkylation of bovine beta-lactoglobulin-bound cysteines exposed to various molar concentrations (0.5-30 mM) of acrylamide and a number of its N-substituted monomers. These measurements were conducted at pH approximately 9.5, and showed that at 0.5 mM all monomers (except N-acryloylaminopropanol) resulted in a measurable alkylation of at least one cysteine out of five. At higher concentrations (15 mM) all investigated monomers resulted in substantial alkylation which, for some, involved all five cysteine residues. Reflectron MALDI-TOF measurements of a number of alkylated protein digests revealed that, at low molar ratios, the alkylation site is influenced by the identity of the monomer. For example acrylamide and N, N-dimethylacrylamide attacked Cys(160) as well as one of the three cysteines within the tryptic fragment [102-124], while other investigated monomers did not involve Cys(160). The implications of the present data for two-dimensional (2D) gel electrophoresis, and their eventual correlation to the toxicity of the investigated monomers, are discussed.

Acrylamides↗
PubMed1991

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.

A method is developed to compute backbone tertiary folds from the amino acid sequence. In this method, the number of degrees of freedom is drastically reduced by neglecting side-chain flexibility, and by describing backbone conformations as combinations of only seven structural states. These are characterized by single values of the dihedral angles phi, psi and omega, representing allowed conformations of the isolated dipeptide. We show that this restrictive model is none the less capable of describing native backbones to within acceptable deviations. Using our backbone description, potentials of mean force are derived from a database of known protein structures, based on statistical influences of single residues and residue pairs on the conformational states in their vicinity along the chain. This yields the force-field component due to local interactions, which is then used to predict lowest-energy conformations from any given amino acid sequence. The prediction algorithm does not require searching conformational space and is therefore extremely fast. Another important asset of our method is that it is able to compute not only the minimum energy conformation, but any number of lowest energy structures, whose relative preferences can be determined from the corresponding computed energy values. The performance of our procedure is tested on short peptides that are likely to be stabilized by local interactions. These include several helical structures and a hexapeptide with a beta-bend conformation, corresponding to peptides shown to have relatively well-defined conformations in aqueous solution, and to protein segments believed to adopt their native conformation early during folding. In addition, several flexible peptides are analysed. Except for the problems encountered in predicting observed disulphide bridges in two of the flexible peptides, and in a somewhat larger fragment comprising residues 30 to 51 of bovine trypsin inhibitor, prediction results compare very favourably with experimental data. Potential applications of our procedure to protein modelling and its extension to protein folding are discussed.

Amino Acid Sequence↗
PubMed1987

A primary genetic linkage map for human chromosome 12.

A primary genetic map for human chromosome 12 has been constructed from data on 23 restriction fragment length polymorphic systems collected in 38 normal families with large sibships. Linkage analysis of the genotypic data has ordered 16 loci into a continuous genetic map of 111 cM in males and 258 cM in females. Although most of the genetic map reflects a higher rate of recombination in females relative to males, significantly more frequent recombination was observed in males than in females in intervals between loci on the distal portion of the short arm of the chromosome. The mapping data shown here will serve as a first step toward a high-resolution genetic map for human chromosome 12.

Animals↗
PubMed1991

Capillary electrophoresis of peptides. Analysis of adrenocorticotropic hormone-related fragments.

Capillary electrophoresis can be used successfully to analyse small peptides to give additional information to that obtained using high-performance liquid chromatography (HPLC). The separation of a modified adrenocorticotropic hormone (4-9) fragment (Org 2766) and several of its fragments was investigated using capillary zone electrophoresis. Prediction of migration in aqueous systems using pKa-related data and the migration behaviour using sodium dodecyl sulphate in the buffer are discussed, as is the choice of buffer systems. The electrophoretic patterns are compared with the HPLC separation.

Adrenocorticotropic Hormone↗