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At least 1,063 records · Page 59Linked to original sources
PubMed1997

Matrix-assisted laser desorption/ionization mass spectrometric peptide mapping of the neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation.

Neurolin is a cell surface protein involved in the neural regeneration and neogenesis of the central nervous system of goldfish. Its theoretical molecular mass, based on the amino acid sequence translated from the cDNA, is 58 kDa, but in SDS-PAGE it shows an apparent MW of 86 kDa. Neurolin is stated to be a glycoprotein and it contains five potential N- and 96 potential O-glycosylation sites. The complete characterization of the primary structure and initial investigations on the postulated glycosylation of neurolin, immunopurified from goldfish brains, are described. The protein was either digested in situ in the sodium dodecyl sulfate polyacrylamide gel matrix or digested after trichloroacetic acid precipitation. Trypsin and endoprotease Glu-C were used as proteases and matrix-assisted laser desorption/ionization mass spectrometry was applied for direct peptide mapping analysis of the proteolytic mixtures. Various sample preparation techniques were performed and the mass spectra were recorded in both positive- and negative-ion modes.

Activated-Leukocyte Cell Adhesion Molecule↗
PubMed1999

Analysis of brain activation patterns using a 3-D scale-space primal sketch.

A fundamental problem in brain imaging concerns how to define functional areas consisting of neurons that are activated together as populations. We propose that this issue can be ideally addressed by a computer vision tool referred to as the scale-space primal sketch. This concept has the attractive properties that it allows for automatic and simultaneous extraction of the spatial extent and the significance of regions with locally high activity. In addition, a hierarchical nested tree structure of activated regions and subregions is obtained. The subject in this article is to show how the scale-space primal sketch can be used for automatic determination of the spatial extent and the significance of rCBF changes. Experiments show the result of applying this approach to functional PET data, including a preliminary comparison with two more traditional clustering techniques. Compared to previous approaches, the method overcomes the limitations of performing the analysis at a single scale or assuming specific models of the data.

Brain Mapping↗
PubMed2000

The therapist-parent alliance in family-based therapy for adolescents.

This article describes procedures for developing a therapeutic alliance with a parent within the context of family therapy for adolescents. After an overview of the general clinical model, specific themes and interventions are described that provide a map to facilitate this process. Following Bordin's (1979) model, alliance is conceptualized in three parts: bonds, goals, and tasks. The bond phase consists of the therapist showing empathy and understanding toward the parent and the parent developing empathy toward their own life struggles. The goal phase consists of defining parent-child relationship building as a primary focus of treatment. The task phase consists of preparing parents to better communicate with their adolescent. These phases can occur sequentially within a single session with a parent alone. The alliance building session sets the foundation for parent-adolescent conflict resolution leading to reattachment in future sessions.

Adolescent↗
PubMed2001

Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry.

Mass spectrometry was applied to identify protein spots excised from an archived two-dimensional polyacrylamide gel that had been dried and stored for eight years at room temperature. All proteins were successfully identified. Detailed characterization of protein digests by matrix-assisted laser desorption/ionization (MALDI) peptide mapping, nanoelectrospray tandem mass spectrometry and MALDI-quadrupole time-of-flight mass spectrometry revealed no evidence of protein degradation or modifications that could hamper identification of proteins in a sequence database. The experiment with a model protein demonstrated that the pattern of tryptic peptides and the yield of individual peptides were not noticeably changed in the in-gel digest of the archived protein spot compared to the digest of the spot excised from a fresh gel. Thus, the characterization of "archived proteomes" has the potential to advance proteomic research without repeating "wet" biochemistry experiments, that had been perfected in the laboratory years ago.

Acrylic Resins↗
PubMed2001

Application of chemical selective cleavage methods to analyze post-translational modification in proteins.

Three chemical specific cleavage reactions, one for the carboxyl side of aspartyl peptide bonds, one for the carboxyl side of asparaginyl peptide bonds and another for the amino side of seryl/threonyl peptide bonds have been recently established. Additionally, these reactions simultaneously react on several post-translationally modified groups in peptides or proteins. The modified groups cover the external modifications N-formyl, N-acetyl, N-pyroglutamyi residues and C-terminal-alpha amide, as well as the internal modifications such as O-acetyl serine, phosphorylated serine/tyrosine, sulfonylated tyrosine, glycosylated serine/threonine and glycosylated asparagine. These three cleavage reactions relate to key amino acids for modifications, deamidation for asparagine, phosphorylation and acetylation for serine, and glycosylation for asparagine, serine and threonine. The chemical reactions on these modifications change the peptide mapping pattern, and information from these reactions may contribute characterization and location of post-translational modified groups in the protein.

Animals↗
PubMedDate not supplied

Mapping gold-labeled receptors on cell surfaces by backscattered electron imaging and digital image analysis: studies of the IgE receptor on mast cells.

The response of cells to signaling molecules such as hormones, growth factors, and immune mediators that bind to cell-surface receptors depends in part on the density and distribution of the relevant receptors. We have developed methods to map the distribution of IgE receptors on RBL-2H3 mast cells at high resolution in the scanning electron microscope (SEM). The key elements of our procedure are a new fixative that preserves receptor binding activity; a family of colloidal gold-conjugated probes that bind directly or indirectly to the IgE-receptor complex; an SEM with detectors for both secondary and backscattered electrons (to observe surface topography and gold particles, respectively); and an image processor that can average, digitize, and store these images. Topographical maps are generated by processing and superimposing the digitized images. The methods we describe can be applied to study the density and distribution of any membrane receptor that can be labeled with colloidal gold particles.

Cell Membrane↗
PubMed1997

The pheromonal role of cuticular hydrocarbons in Drosophila melanogaster.

Pheromones play a crucial role in mate stimulation and discrimination. In the fruit fly Drosophila, the most abundant cuticular hydrocarbons act as sex pheromones during courtship behavior. There are several active molecules and they compose a sex- and species-specific pheromonal bouquet. Different species from the Drosophila melanogaster subgroup have adopted alternative systems of chemical mate recognition. Recent exploration of these interspecific variations, and of intraspecific variations, has led to the characterization of genes and to the mapping of structures that process the production and perception of chemical messages.

Alkadienes↗
PubMed1991

The effect of TTX-activity blockade and total darkness on the formation of retinotopy in the goldfish retinotectal projection.

In the normal goldfish, neighboring retinal ganglion cells terminate in one small tectal locus to produce the precise retinotopy characteristic of this projection. This can be directly demonstrated by labeling neighboring ganglion cells with small "spot" injections of WGA-HRP, which yield a single small patch of product at the retinotopically appropriate part of the tectum. When the optic nerve is crushed, label from these spot injections was previously found to be widely dispersed during the early phase of regeneration. With time, label subsequently condensed, typically into several discrete patches reminiscent of ocular dominance columns. In this study, we tested whether the formation of these patches required impulse activity by injecting tetrodotoxin (TTX) into the eye during regeneration. We found that impulse blockade completely inhibited the formation of discrete patches while permitting considerable condensation of the label. This implies that these patches are generated by activity but that some map "refinement" utilized cellular processes that are activity independent. This activity-independent condensation progressed at a noticeably slower rate than the equivalent condensation seen with activity, thus suggesting that activity normally participates as a "helper factor," even though it is not strictly required. Since the formation of discrete patches during regeneration provides a sensitive measure of activity-dependent refinement, this was used to further address two controversial questions concerning the role of impulse activity. One is whether there is a chronologically defined critical period for activity-dependent refinement. This was tested by blocking impulse activity for 2 to 4 months, much longer than the activity-dependent refinement is thought to last, and then permitting activity to resume. We found that multiple patches were formed following this period of late activity, thus indicating that synaptic plasticity extends for several months beyond the supposed critical period. The other question was whether spontaneous retinal activity was sufficient for activity-dependent ordering. To test this, fish were kept in constant darkness during optic nerve crush and labelled with retinal spot injections at various times during regeneration. Condensation of label with the final formation of multiple patches formed at about the same time as fish with normal visual experience. This implies that the amount and extent of correlation of spontaneous activity in retina is adequate for driving activity-dependent refinement.

Animals↗
PubMed1994

Activation of phosphatidylinositol-3-kinase in Jurkat T cells depends on the presence of the p56lck tyrosine kinase.

Activation of resting T lymphocytes by ligands to the T cell receptor (TcR)/CD3 complex is initiated by phosphorylation of a number of key regulatory proteins on specific tyrosine residues. One such protein is the heterodimeric enzyme phosphatidylinositol-3-kinase (PI3K). We recently found that this enzyme is also rapidly activated following TcR/CD3 triggering and that immunoprecipitated PI3K was activated in vitro by direct tyrosine phosphorylation. Here we show that TcR/CD3-induced tyrosine phosphorylation and activation of PI3K in Jurkat T leukemia cells depend on the presence of the p56lck tyrosine kinase: in a variant of the Jurkat T cell line lacking p56lck, JCaM1, these responses were absent. We also show that p56lck directly activates PI3K purified from transfected COS-1 cells, indicating that other T cell-specific proteins are not required for the process. Finally, tryptic peptide maps show that p56lck phosphorylates three tyrosine residues in the p85 alpha subunit of PI3K and two in p110 of PI3K. Our results suggest that p56lck is required for activation of PI3K in Jurkat T cells and can itself directly activate it by phosphorylating one or several stimulatory sites.

Enzyme Activation↗
PubMed1990

Murine lambda gene rearrangements: the stochastic model prevails over the ordered model.

The ontogeny of the immunoglobulin (Ig) gene rearrangement in mammalian B cells seems to be ordered. Heavy chain gene segments rearrange first, followed by light chain gene segments, kappa before lambda. The genomic organization of murine lambda locus does not preclude the simultaneous expression of two subtypes from the same chromosome. In order to distinguish between an ordered and a stochastic model of rearrangement, a panel of 67 B cell hybridomas secreting either lambda 1, lambda 2, lambda 3 or lambda x (recently described) were analysed for V lambda J lambda rearrangements. The results show that in 97% of cases, a single rearrangement occurred, favouring the stochastic model over the ordered one. Strikingly, the possibility of having a productive rearrangement if the first try results in an aberrant one is rare. We propose therefore, that the lambda Ig is not necessarily required to ensure allelic and subtypic exclusion mechanisms. Moreover, in 97% of the cases, at least one kappa allele is rearranged. Furthermore, the RS recombination has been detected in 77% of the cases. This suggests that, although the stimulation of kappa precedes that of lambda locus, the RS recombination acts as a transacting albeit dispensable lambda activator.

Animals↗
PubMed2004

Application of mass spectrometry to the identification and quantification of histone post-translational modifications.

The core histones are the primary protein component of chromatin, which is responsible for the packaging of eukaryotic DNA. The NH(2)-terminal tail domains of the core histones are the sites of numerous post-translational modifications that have been shown to play an important role in the regulation of chromatin structure. In this study, we discuss the recent application of modern analytical techniques to the study of histone modifications. Through the use of mass spectrometry, a large number of new sites of histone modification have been identified, many of which reside outside of the NH(2)-terminal tail domains. In addition, techniques have been developed that allow mass spectrometry to be effective for the quantitation of histone post-translational modifications. Hence, the use of mass spectrometry promises to dramatically alter our view of histone post-translational modifications.

Animals↗
PubMed1989

Posttranslational insertion of a membrane protein on Caenorhabditis elegans sperm occurs without de novo protein synthesis.

We have examined the mechanism of membrane protein insertion in the ameboid spermatozoa of Caenorhabditis elegans using two monoclonal antibodies which recognize the same set of eight sperm-specific polypeptides. Previous electron microscopic studies demonstrated that these antibodies label surface and cytoplasmic populations of antigen. Cells whose surface antigen had been removed by proteolysis were able to localize new membrane protein insertion at the tips of pseudopodial projections. C. elegans sperm do not contain the protein synthesizing machinery needed for delivery of new membrane to the cell surface. It has, therefore, been of interest to determine how localized membrane assembly occurs. Here we have determined the subcellular location of each of these eight polypeptides. A closely positioned doublet of bands around 97 kD (comprising 40% of the total antigen in sperm) represents surface (larger member of doublet) and cytoplasmic (lower member) forms of protein. Proteolysis of live cells eliminated this surface form from immunoblots but did not affect the cytoplasmic protein. When cells were allowed to reinsert new protein following removal of the enzyme, this surface form was regenerated. Since sperm are unable to synthesize new protein, this higher molecular weight species may arise from a posttranslational modification of proteins in the cytoplasmic pool. We present evidence suggesting that the surface protein is generated from this cytoplasmic pool by addition of fatty acid. Fatty acid acylation would account for both the observed decrease in electrophoretic mobility of the surface form and provide increased hydrophobicity to the protein which may allow for its insertion into the lipid bilayer.

Animals↗
PubMedDate not supplied

The application of the acoustic spectrophonometer to biomolecular spectrometry: a step towards acoustic "fingerprinting".

A tunable acoustic biosensor for investigating the properties of biomolecules at the solid-liquid interfaces is described. In its current, format the device can be tuned to frequencies between 6.5 MHz and 1.1 GHz in order to provide a unique detection feature: a variable evanescent wave thickness at the sensor surface. The key to its successful implementation required the careful selection of antennae designs that could induce shear acoustic waves at the solid-liquid interface. This non-contact format makes it possible to recover resonant shear acoustic waves over 100 different harmonic frequencies as a result of the electrical characteristics of the spiral coil. For testing this multifrequency sensing concept the surface of a quartz disc was exposed to solutions of immunoglobulin G (IgG) to form an adsorbed monolayer, whence protein A and IgG were added again in order to form multilayers. Spectra at frequencies between 6 and 600 MHz were generated for each successive layer and revealed two characteristic phases: an initial phase at the low megahertz frequencies consistent with the conventional Sauerbrey relation, and a possible additional phase towards the high megahertz to gigahertz frequencies, that we believe relates to the structure of the biomolecular film. This two-phase behaviour evident from differences between high and low frequencies, rather than from any distinct frequency transition, was anticipated from the reduction in evanescent wave thickness down to nanometre dimensions, and thin film resonance phenomena that are known to occur for film and fluid systems. These measurements suggested that the single element acoustic biosensor we present here may form the basis from which to generate acoustic molecular spectra, or "acoustic fingerprints", in a manner akin to optical spectroscopy.

Acoustics↗
PubMed2006

Posttranslational modifications of collagen studied by off-line coupling of HPLC and CE.

A typical example of non-enzymatic change of collagen is glycation (the Maillard reaction, formation of advanced glycation end products) resulting from the reaction of sugars with the epsilon-amino group of lysine. Posttranslational non-enzymatic modifications of collagen by sugars were studied. Collagenous tissues were incubated as a test protein separately with both glucose and ribose. The collagen mixture was digested by bacterial collagenase and separated by reversed-phase HPLC (in a Jupiter Proteo 90 A column). The eluate from this HPLC separation was collected as seven fractions and consecutively analysed by CE in a bare fused silica capillary (57/50 cm x 75 mm id) using 100 mM sodium 1-heptanesulfonate in 100 mM phosphate buffer, pH 2.5 (NaH2PO4 adjusted to pH by phosphoric acid). The chromatographic and electromigration behaviour of individual peptides varied considerably. This off-line HPLC-CE coupling made it possible to discover minor changes in the structure of collagen caused by posttranslational modifications. A new HPLC-CE technique for peptide analysis was developed, and applied to the identification of posttranslational modifications in slowly metabolised test proteins.

Animals↗
PubMed1992

Porcine oocyte zona pellucida M(r) 55,000 glycoproteins: identification of O-glycosylated domains.

The distribution of O-linked oligosaccharides on the M(r) 55,000 glycoproteins, ZP3 alpha and ZP3 beta, of the porcine oocyte zona pellucida was examined. Purified preparations of endo-beta-galactosidase digested ZP3 alpha and ZP3 beta were reduced and carboxamidomethylated and digested with trypsin. When the trypsin digests were mapped by HPLC, each glycoprotein yielded only one N-acetylgalactosamine containing glycopeptide. Purification of the O-glycopeptides was achieved by a two-step protocol. Tryptic digests were applied to jacalin-agarose and specifically-bound O-glycopeptides (alpha OGP and beta OGP) were eluted with buffer containing 50 mM alpha-methylgalactoside as the haptenic sugar. Further purification of each O-glycopeptide was accomplished by reverse phase HPLC. Purified O-glycopeptides were characterized with respect to amino acid and carbohydrate compositions and sequenced by automated Edman degradation; alpha OGP was a 41-residue glycopeptide with three O-linked sugar chains. Sequence comparisons revealed a 75% identity between alpha OGP and a corresponding segment of rabbit rec55 zona protein; beta OGP was a 25-residue glycopeptide characterized by the presence of one N-linked and five O-linked sugar chains and a trypsin-resistant internal arginine residue. Sequence alignments revealed an 80% or greater identity between beta OGP and internal peptides of mouse, hamster and human ZP3 zona proteins. These studies demonstrate that in the case of ZP3 alpha and ZP3 beta, the pig homologues of rabbit rec55 and mouse ZP3, respectively, O-linked oligosaccharides are confined within delimited domains rather than widely dispersed on the polypeptide backbone. Such clustering of O-linked oligosaccharides may represent an essential determinant of the structure and biological activity of zona proteins.

Amino Acid Sequence↗
PubMed2001

Single-shot diffusion trace (1)H NMR spectroscopy.

Ignoring diffusion anisotropy can severely hamper the quantitative determination of water and metabolite diffusion in complex tissues. The measurement of the trace of the diffusion tensor provides unambiguous and rotationally invariant ADC values, but usually requires three separate experiments. A single-shot technique developed earlier, originally designed for diffusion trace MR imaging (Mori and van Zijl, Magn Reson Med 1995;33:41-52), was improved and adapted for diffusion trace MR spectroscopy. A double spin-echo pulse sequence was incorporated with four pairs of bipolar gradients with specific predetermined relative signs in each of the three orthogonal directions. The combination of gradient directions leads to cancellation of all off-diagonal tensor elements while constructively adding the diagonal elements. Furthermore, the pulse scheme provides complete compensation for cross-terms between static magnetic field gradients and the applied diffusion gradients, while simultaneously avoiding cross-terms with localization gradients. The sequence was tested at 4.7 T in vivo on rat brain for MRI and on rat skeletal muscle and brain for MRS. It is shown that the average ADC as determined from the measurement of the ADCs in the three orthogonal directions is in close agreement with the ADC obtained along the trace of the diffusion tensor in a single acquisition, for both water and metabolite diffusion. The large differences in water and metabolite diffusion coefficients as measured in the individual orthogonal directions illustrate the need for diffusion trace measurements when accurate and rotationally invariant diffusion quantitation is required. The pulse scheme presented here may be applied for such purposes in MRS and MRI studies.

Algorithms↗
PubMed2004

A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications.

The N-terminal tails of the histones are subject to many enzyme-mediated post-translational modifications, such as lysine acetylation, lysine and arginine methylation, serine phosphorylation, poly-ADP ribosylation and the attachment of the small peptide ubiquitin. These modifications, singly or in combination, are thought to generate an epigenetic code that specifies different patterns of gene activity. We present a detailed study on the mapping of histone post-translational modifications using a combination of matrix-assisted laser desorption/ionization-time of flight and electrospray ionization tandem mass spectrometry analysis of peptides generated by protease cleavage of individual histones isolated from different developmental stages. Due to their high content in basic amino acid residues and in order to be able to quantitatively compare two different samples we developed a chemical derivatization protocol. This strategy enabled us to determine the primary sequence of the peptides and to unambiguously assign specific modifications. This method is generally applicable to histone samples from various sources and can be used to study changes of modification patterns during early embryonic development or tissue differentiation and regeneration.

Amino Acid Sequence↗